diff --git a/doc/displace_atoms.html b/doc/displace_atoms.html
index 727f55007..86c82fbf2 100644
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<div class="section" id="displace-atoms-command">
<span id="index-0"></span><h1>displace_atoms command<a class="headerlink" href="#displace-atoms-command" title="Permalink to this headline">¶</a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
<div class="highlight-python"><div class="highlight"><pre>displace_atoms group-ID style args keyword value ...
</pre></div>
</div>
<ul class="simple">
<li>group-ID = ID of group of atoms to displace</li>
<li>style = <em>move</em> or <em>ramp</em> or <em>random</em> or <em>rotate</em></li>
</ul>
<pre class="literal-block">
<em>move</em> args = delx dely delz
delx,dely,delz = distance to displace in each dimension (distance units)
any of delx,dely,delz can be a variable (see below)
<em>ramp</em> args = ddim dlo dhi dim clo chi
ddim = <em>x</em> or <em>y</em> or <em>z</em>
dlo,dhi = displacement distance between dlo and dhi (distance units)
dim = <em>x</em> or <em>y</em> or <em>z</em>
clo,chi = lower and upper bound of domain to displace (distance units)
<em>random</em> args = dx dy dz seed
dx,dy,dz = random displacement magnitude in each dimension (distance units)
seed = random # seed (positive integer)
<em>rotate</em> args = Px Py Pz Rx Ry Rz theta
Px,Py,Pz = origin point of axis of rotation (distance units)
Rx,Ry,Rz = axis of rotation vector
theta = angle of rotation (degrees)
</pre>
<ul class="simple">
<li>zero or more keyword/value pairs may be appended</li>
</ul>
<pre class="literal-block">
keyword = <em>units</em>
value = <em>box</em> or <em>lattice</em>
</pre>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
<div class="highlight-python"><div class="highlight"><pre>displace_atoms top move 0 -5 0 units box
displace_atoms flow ramp x 0.0 5.0 y 2.0 20.5
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>Displace a group of atoms. This can be used to move atoms a large
distance before beginning a simulation or to randomize atoms initially
on a lattice. For example, in a shear simulation, an initial strain
can be imposed on the system. Or two groups of atoms can be brought
into closer proximity.</p>
<p>The <em>move</em> style displaces the group of atoms by the specified 3d
displacement vector. Any of the 3 quantities defining the vector
components can be specified as an equal-style or atom-style
<a class="reference internal" href="variable.html"><em>variable</em></a>. If the value is a variable, it should be
specified as v_name, where name is the variable name. In this case,
the variable will be evaluated, and its value(s) used for the
displacement(s). The scale factor implied by the <em>units</em> keyword will
also be applied to the variable result.</p>
<p>Equal-style variables can specify formulas with various mathematical
functions, and include <a class="reference internal" href="thermo_style.html"><em>thermo_style</em></a> command
keywords for the simulation box parameters and timestep and elapsed
time. Atom-style variables can specify the same formulas as
equal-style variables but can also include per-atom values, such as
atom coordinates or per-atom values read from a file. Note that if
the variable references other <a class="reference internal" href="compute.html"><em>compute</em></a> or <a class="reference internal" href="fix.html"><em>fix</em></a>
commands, those values must be up-to-date for the current timestep.
See the “Variable Accuracy” section of the <a class="reference internal" href="variable.html"><em>variable</em></a>
doc page for more details.</p>
<p>The <em>ramp</em> style displaces atoms a variable amount in one dimension
depending on the atom’s coordinate in a (possibly) different
dimension. For example, the second example command displaces atoms in
the x-direction an amount between 0.0 and 5.0 distance units. Each
atom’s displacement depends on the fractional distance its y
coordinate is between 2.0 and 20.5. Atoms with y-coordinates outside
those bounds will be moved the minimum (0.0) or maximum (5.0) amount.</p>
<p>The <em>random</em> style independently moves each atom in the group by a
random displacement, uniformly sampled from a value between -dx and
+dx in the x dimension, and similarly for y and z. Random numbers are
used in such a way that the displacement of a particular atom is the
same, regardless of how many processors are being used.</p>
<p>The <em>rotate</em> style rotates each atom in the group by the angle <em>theta</em>
around a rotation axis <em>R</em> = (Rx,Ry,Rz) that goes thru a point <em>P</em> =
(Px,Py,Pz). The direction of rotation for the atoms around the
rotation axis is consistent with the right-hand rule: if your
-right-hand’s thumb points along <em>R</em>, then your fingers wrap around the
+right-hand thumb points along <em>R</em>, then your fingers wrap around the
axis in the direction of positive theta.</p>
+<p>If the defined <a class="reference internal" href="atom_style.html"><em>atom_style</em></a> assigns an orientation to
+each atom (<a class="reference internal" href="atom_style.html"><em>atom styles</em></a> ellipsoid, line, tri, body),
+then that property is also updated appropriately to correspond to the
+atom’s rotation.</p>
<p>Distance units for displacements and the origin point of the <em>rotate</em>
style are determined by the setting of <em>box</em> or <em>lattice</em> for the
<em>units</em> keyword. <em>Box</em> means distance units as defined by the
<a class="reference internal" href="units.html"><em>units</em></a> command - e.g. Angstroms for <em>real</em> units.
<em>Lattice</em> means distance units are in lattice spacings. The
<a class="reference internal" href="lattice.html"><em>lattice</em></a> command must have been previously used to
define the lattice spacing.</p>
<hr class="docutils" />
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Care should be taken not to move atoms on top of other atoms.
After the move, atoms are remapped into the periodic simulation box if
needed, and any shrink-wrap boundary conditions (see the
<a class="reference internal" href="boundary.html"><em>boundary</em></a> command) are enforced which may change the
box size. Other than this effect, this command does not change the
size or shape of the simulation box. See the
<a class="reference internal" href="change_box.html"><em>change_box</em></a> command if that effect is desired.</p>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Atoms can be moved arbitrarily long distances by this command.
If the simulation box is non-periodic and shrink-wrapped (see the
<a class="reference internal" href="boundary.html"><em>boundary</em></a> command), this can change its size or shape.
This is not a problem, except that the mapping of processors to the
simulation box is not changed by this command from its initial 3d
configuration; see the <a class="reference internal" href="processors.html"><em>processors</em></a> command. Thus, if
the box size/shape changes dramatically, the mapping of processors to
the simulation box may not end up as optimal as the initial mapping
attempted to be.</p>
</div>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
<p>You cannot rotate around any rotation vector except the z-axis for a
2d simulation.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
<p><a class="reference internal" href="lattice.html"><em>lattice</em></a>, <a class="reference internal" href="change_box.html"><em>change_box</em></a>,
<a class="reference internal" href="fix_move.html"><em>fix_move</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
<p>The option defaults are units = lattice.</p>
</div>
</div>
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diff --git a/doc/displace_atoms.txt b/doc/displace_atoms.txt
index 3bb1f1a2d..2df01ccf6 100644
--- a/doc/displace_atoms.txt
+++ b/doc/displace_atoms.txt
@@ -1,134 +1,139 @@
"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
displace_atoms command :h3
[Syntax:]
displace_atoms group-ID style args keyword value ... :pre
group-ID = ID of group of atoms to displace :ulb,l
style = {move} or {ramp} or {random} or {rotate} :l
{move} args = delx dely delz
delx,dely,delz = distance to displace in each dimension (distance units)
any of delx,dely,delz can be a variable (see below)
{ramp} args = ddim dlo dhi dim clo chi
ddim = {x} or {y} or {z}
dlo,dhi = displacement distance between dlo and dhi (distance units)
dim = {x} or {y} or {z}
clo,chi = lower and upper bound of domain to displace (distance units)
{random} args = dx dy dz seed
dx,dy,dz = random displacement magnitude in each dimension (distance units)
seed = random # seed (positive integer)
{rotate} args = Px Py Pz Rx Ry Rz theta
Px,Py,Pz = origin point of axis of rotation (distance units)
Rx,Ry,Rz = axis of rotation vector
theta = angle of rotation (degrees) :pre
zero or more keyword/value pairs may be appended :l
keyword = {units}
value = {box} or {lattice} :pre
:ule
[Examples:]
displace_atoms top move 0 -5 0 units box
displace_atoms flow ramp x 0.0 5.0 y 2.0 20.5 :pre
[Description:]
Displace a group of atoms. This can be used to move atoms a large
distance before beginning a simulation or to randomize atoms initially
on a lattice. For example, in a shear simulation, an initial strain
can be imposed on the system. Or two groups of atoms can be brought
into closer proximity.
The {move} style displaces the group of atoms by the specified 3d
displacement vector. Any of the 3 quantities defining the vector
components can be specified as an equal-style or atom-style
"variable"_variable.html. If the value is a variable, it should be
specified as v_name, where name is the variable name. In this case,
the variable will be evaluated, and its value(s) used for the
displacement(s). The scale factor implied by the {units} keyword will
also be applied to the variable result.
Equal-style variables can specify formulas with various mathematical
functions, and include "thermo_style"_thermo_style.html command
keywords for the simulation box parameters and timestep and elapsed
time. Atom-style variables can specify the same formulas as
equal-style variables but can also include per-atom values, such as
atom coordinates or per-atom values read from a file. Note that if
the variable references other "compute"_compute.html or "fix"_fix.html
commands, those values must be up-to-date for the current timestep.
See the "Variable Accuracy" section of the "variable"_variable.html
doc page for more details.
The {ramp} style displaces atoms a variable amount in one dimension
depending on the atom's coordinate in a (possibly) different
dimension. For example, the second example command displaces atoms in
the x-direction an amount between 0.0 and 5.0 distance units. Each
atom's displacement depends on the fractional distance its y
coordinate is between 2.0 and 20.5. Atoms with y-coordinates outside
those bounds will be moved the minimum (0.0) or maximum (5.0) amount.
The {random} style independently moves each atom in the group by a
random displacement, uniformly sampled from a value between -dx and
+dx in the x dimension, and similarly for y and z. Random numbers are
used in such a way that the displacement of a particular atom is the
same, regardless of how many processors are being used.
The {rotate} style rotates each atom in the group by the angle {theta}
around a rotation axis {R} = (Rx,Ry,Rz) that goes thru a point {P} =
(Px,Py,Pz). The direction of rotation for the atoms around the
rotation axis is consistent with the right-hand rule: if your
-right-hand's thumb points along {R}, then your fingers wrap around the
+right-hand thumb points along {R}, then your fingers wrap around the
axis in the direction of positive theta.
+If the defined "atom_style"_atom_style.html assigns an orientation to
+each atom ("atom styles"_atom_style.html ellipsoid, line, tri, body),
+then that property is also updated appropriately to correspond to the
+atom's rotation.
+
Distance units for displacements and the origin point of the {rotate}
style are determined by the setting of {box} or {lattice} for the
{units} keyword. {Box} means distance units as defined by the
"units"_units.html command - e.g. Angstroms for {real} units.
{Lattice} means distance units are in lattice spacings. The
"lattice"_lattice.html command must have been previously used to
define the lattice spacing.
:line
NOTE: Care should be taken not to move atoms on top of other atoms.
After the move, atoms are remapped into the periodic simulation box if
needed, and any shrink-wrap boundary conditions (see the
"boundary"_boundary.html command) are enforced which may change the
box size. Other than this effect, this command does not change the
size or shape of the simulation box. See the
"change_box"_change_box.html command if that effect is desired.
NOTE: Atoms can be moved arbitrarily long distances by this command.
If the simulation box is non-periodic and shrink-wrapped (see the
"boundary"_boundary.html command), this can change its size or shape.
This is not a problem, except that the mapping of processors to the
simulation box is not changed by this command from its initial 3d
configuration; see the "processors"_processors.html command. Thus, if
the box size/shape changes dramatically, the mapping of processors to
the simulation box may not end up as optimal as the initial mapping
attempted to be.
:line
[Restrictions:]
You cannot rotate around any rotation vector except the z-axis for a
2d simulation.
[Related commands:]
"lattice"_lattice.html, "change_box"_change_box.html,
"fix_move"_fix_move.html
[Default:]
The option defaults are units = lattice.
diff --git a/doc/dump_image.html b/doc/dump_image.html
index 8a2f4a918..05e17d0ac 100644
--- a/doc/dump_image.html
+++ b/doc/dump_image.html
@@ -1,727 +1,774 @@
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<div class="section" id="dump-image-command">
<span id="index-0"></span><h1>dump image command<a class="headerlink" href="#dump-image-command" title="Permalink to this headline">¶</a></h1>
</div>
<div class="section" id="dump-movie-command">
<h1>dump movie command<a class="headerlink" href="#dump-movie-command" title="Permalink to this headline">¶</a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
<div class="highlight-python"><div class="highlight"><pre>dump ID group-ID style N file color diameter keyword value ...
</pre></div>
</div>
<ul class="simple">
<li>ID = user-assigned name for the dump</li>
<li>group-ID = ID of the group of atoms to be imaged</li>
<li>style = <em>image</em> or <em>movie</em> = style of dump command (other styles <em>atom</em> or <em>cfg</em> or <em>dcd</em> or <em>xtc</em> or <em>xyz</em> or <em>local</em> or <em>custom</em> are discussed on the <a class="reference internal" href="dump.html"><em>dump</em></a> doc page)</li>
<li>N = dump every this many timesteps</li>
<li>file = name of file to write image to</li>
<li>color = atom attribute that determines color of each atom</li>
<li>diameter = atom attribute that determines size of each atom</li>
<li>zero or more keyword/value pairs may be appended</li>
-<li>keyword = <em>adiam</em> or <em>atom</em> or <em>body</em> or <em>bond</em> or <em>size</em> or <em>view</em> or <em>center</em> or <em>up</em> or <em>zoom</em> or <em>persp</em> or <em>box</em> or <em>axes</em> or <em>subbox</em> or <em>shiny</em> or <em>ssao</em></li>
+<li>keyword = <em>atom</em> or <em>adiam</em> or <em>bond</em> or <em>line</em> or <em>tri</em> or <em>body</em> or <em>size</em> or <em>view</em> or <em>center</em> or <em>up</em> or <em>zoom</em> or <em>persp</em> or <em>box</em> or <em>axes</em> or <em>subbox</em> or <em>shiny</em> or <em>ssao</em></li>
</ul>
<pre class="literal-block">
-<em>adiam</em> value = number = numeric value for atom diameter (distance units)
<em>atom</em> = yes/no = do or do not draw atoms
-<em>body</em> = yes/no bflag1 bflag2
- yes/no = do or do not draw atoms as bodies
- bflag1,bflag2 = 2 numeric flags to affect how bodies are drawn
+<em>adiam</em> size = numeric value for atom diameter (distance units)
<em>bond</em> values = color width = color and width of bonds
color = <em>atom</em> or <em>type</em> or <em>none</em>
width = number or <em>atom</em> or <em>type</em> or <em>none</em>
number = numeric value for bond width (distance units)
+<em>line</em> = color width
+ color = <em>type</em>
+ width = numeric value for line width (distance units)
+<em>tri</em> = color
+ color = <em>type</em>
+<em>body</em> = color bflag1 bflag2
+ color = <em>type</em>
+ bflag1,bflag2 = 2 numeric flags to affect how bodies are drawn
<em>size</em> values = width height = size of images
width = width of image in # of pixels
height = height of image in # of pixels
<em>view</em> values = theta phi = view of simulation box
theta = view angle from +z axis (degrees)
phi = azimuthal view angle (degrees)
theta or phi can be a variable (see below)
<em>center</em> values = flag Cx Cy Cz = center point of image
flag = "s" for static, "d" for dynamic
Cx,Cy,Cz = center point of image as fraction of box dimension (0.5 = center of box)
Cx,Cy,Cz can be variables (see below)
<em>up</em> values = Ux Uy Uz = direction that is "up" in image
Ux,Uy,Uz = components of up vector
Ux,Uy,Uz can be variables (see below)
<em>zoom</em> value = zfactor = size that simulation box appears in image
zfactor = scale image size by factor > 1 to enlarge, factor < 1 to shrink
zfactor can be a variable (see below)
<em>persp</em> value = pfactor = amount of "perspective" in image
pfactor = amount of perspective (0 = none, < 1 = some, > 1 = highly skewed)
pfactor can be a variable (see below)
<em>box</em> values = yes/no diam = draw outline of simulation box
yes/no = do or do not draw simulation box lines
diam = diameter of box lines as fraction of shortest box length
<em>axes</em> values = yes/no length diam = draw xyz axes
yes/no = do or do not draw xyz axes lines next to simulation box
length = length of axes lines as fraction of respective box lengths
diam = diameter of axes lines as fraction of shortest box length
<em>subbox</em> values = yes/no diam = draw outline of processor sub-domains
yes/no = do or do not draw sub-domain lines
diam = diameter of sub-domain lines as fraction of shortest box length
<em>shiny</em> value = sfactor = shinyness of spheres and cylinders
sfactor = shinyness of spheres and cylinders from 0.0 to 1.0
<em>ssao</em> value = yes/no seed dfactor = SSAO depth shading
yes/no = turn depth shading on/off
seed = random # seed (positive integer)
dfactor = strength of shading from 0.0 to 1.0
</pre>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
<div class="highlight-python"><div class="highlight"><pre>dump d0 all image 100 dump.*.jpg type type
dump d1 mobile image 500 snap.*.png element element ssao yes 4539 0.6
dump d2 all image 200 img-*.ppm type type zoom 2.5 adiam 1.5 size 1280 720
dump m0 all movie 1000 movie.mpg type type size 640 480
dump m1 all movie 1000 movie.avi type type size 640 480
dump m2 all movie 100 movie.m4v type type zoom 1.8 adiam v_value size 1280 720
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>Dump a high-quality rendered image of the atom configuration every N
timesteps and save the images either as a sequence of JPEG or PNG or
PPM files, or as a single movie file. The options for this command as
well as the <a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a> command control what is
included in the image or movie and how it appears. A series of such
images can easily be manually converted into an animated movie of your
simulation or the process can be automated without writing the
intermediate files using the dump movie style; see further details
below. Other dump styles store snapshots of numerical data asociated
with atoms in various formats, as discussed on the <a class="reference internal" href="dump.html"><em>dump</em></a>
doc page.</p>
<p>Note that a set of images or a movie can be made after a simulation
has been run, using the <a class="reference internal" href="rerun.html"><em>rerun</em></a> command to read snapshots
from an existing dump file, and using these dump commands in the rerun
script to generate the images/movie.</p>
<p>Here are two sample images, rendered as 1024x1024 JPEG files. Click
to see the full-size images:</p>
<DIV ALIGN=center><a data-lightbox="group-default"
href="_images/dump1.jpg"
class=""
title=""
data-title=""
><img src="_images/dump1.jpg"
class=""
width="25%"
height="auto"
alt=""/>
</a><a data-lightbox="group-default"
href="_images/dump2.jpg"
class=""
title=""
data-title=""
><img src="_images/dump2.jpg"
class=""
width="25%"
height="auto"
alt=""/>
</a></DIV><p>Only atoms in the specified group are rendered in the image. The
<a class="reference internal" href="dump_modify.html"><em>dump_modify region and thresh</em></a> commands can also
alter what atoms are included in the image.
The filename suffix determines whether a JPEG, PNG, or PPM file is
created with the <em>image</em> dump style. If the suffix is ”.jpg” or
”.jpeg”, then a JPEG format file is created, if the suffix is ”.png”,
then a PNG format is created, else a PPM (aka NETPBM) format file is
created. The JPEG and PNG files are binary; PPM has a text mode
header followed by binary data. JPEG images have lossy compression;
PNG has lossless compression; and PPM files are uncompressed but can
be compressed with gzip, if LAMMPS has been compiled with
-DLAMMPS_GZIP and a ”.gz” suffix is used.</p>
<p>Similarly, the format of the resulting movie is chosen with the
<em>movie</em> dump style. This is handled by the underlying FFmpeg converter
and thus details have to be looked up in the FFmpeg documentation.
Typical examples are: .avi, .mpg, .m4v, .mp4, .mkv, .flv, .mov, .gif
Additional settings of the movie compression like bitrate and
framerate can be set using the <a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a> command.</p>
<p>To write out JPEG and PNG format files, you must build LAMMPS with
support for the corresponding JPEG or PNG library. To convert images
into movies, LAMMPS has to be compiled with the -DLAMMPS_FFMPEG
flag. See <a class="reference internal" href="Section_start.html#start-2-4"><span>this section</span></a> of the manual
for instructions on how to do this.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Because periodic boundary conditions are enforced only on
timesteps when neighbor lists are rebuilt, the coordinates of an atom
in the image may be slightly outside the simulation box.</p>
</div>
<hr class="docutils" />
<p>Dumps are performed on timesteps that are a multiple of N (including
timestep 0) and on the last timestep of a minimization if the
minimization converges. Note that this means a dump will not be
performed on the initial timestep after the dump command is invoked,
if the current timestep is not a multiple of N. This behavior can be
changed via the <a class="reference internal" href="dump_modify.html"><em>dump_modify first</em></a> command, which
can be useful if the dump command is invoked after a minimization
ended on an arbitrary timestep. N can be changed between runs by
using the <a class="reference internal" href="dump_modify.html"><em>dump_modify every</em></a> command.</p>
<p>Dump <em>image</em> filenames must contain a wildcard character “*”, so that
one image file per snapshot is written. The “*” character is replaced
with the timestep value. For example, tmp.dump.*.jpg becomes
tmp.dump.0.jpg, tmp.dump.10000.jpg, tmp.dump.20000.jpg, etc. Note
that the <a class="reference internal" href="dump_modify.html"><em>dump_modify pad</em></a> command can be used to
insure all timestep numbers are the same length (e.g. 00010), which
can make it easier to convert a series of images into a movie in the
correct ordering.</p>
<p>Dump <em>movie</em> filenames on the other hand, must not have any wildcard
character since only one file combining all images into a single
movie will be written by the movie encoder.</p>
<hr class="docutils" />
<p>The <em>color</em> and <em>diameter</em> settings determine the color and size of
atoms rendered in the image. They can be any atom attribute defined
for the <a class="reference internal" href="dump.html"><em>dump custom</em></a> command, including <em>type</em> and
<em>element</em>. This includes per-atom quantities calculated by a
<a class="reference internal" href="compute.html"><em>compute</em></a>, <a class="reference internal" href="fix.html"><em>fix</em></a>, or <a class="reference internal" href="variable.html"><em>variable</em></a>,
which are prefixed by “<a href="#id9"><span class="problematic" id="id10">c_</span></a>”, “<a href="#id11"><span class="problematic" id="id12">f_</span></a>”, or “<a href="#id13"><span class="problematic" id="id14">v_</span></a>” respectively. Note that the
<em>diameter</em> setting can be overridden with a numeric value applied to
all atoms by the optional <em>adiam</em> keyword.</p>
<p>If <em>type</em> is specified for the <em>color</em> setting, then the color of each
atom is determined by its atom type. 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>
<li>type 3 = blue</li>
<li>type 4 = yellow</li>
<li>type 5 = aqua</li>
<li>type 6 = cyan</li>
</ul>
<p>and repeats itself for types > 6. This mapping can be changed by the
<a class="reference internal" href="dump_modify.html"><em>dump_modify acolor</em></a> command.</p>
<p>If <em>type</em> is specified for the <em>diameter</em> setting then the diameter of
each atom is determined by its atom type. By default all types have
diameter 1.0. This mapping can be changed by the <a class="reference internal" href="dump_modify.html"><em>dump_modify adiam</em></a> command.</p>
<p>If <em>element</em> is specified for the <em>color</em> and/or <em>diameter</em> setting,
then the color and/or diameter of each atom is determined by which
element it is, which in turn is specified by the element-to-type
mapping specified by the “dump_modify element” command. By default
every atom type is C (carbon). Every element has a color and diameter
associated with it, which is the same as the colors and sizes used by
the <a class="reference external" href="http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</a> visualization package.</p>
<p>If other atom attributes are used for the <em>color</em> or <em>diameter</em>
settings, they are interpreted in the following way.</p>
<p>If “vx”, for example, is used as the <em>color</em> setting, then the color
of the atom will depend on the x-component of its velocity. The
association of a per-atom value with a specific color is determined by
a “color map”, which can be specified via the
<a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a> command. The basic idea is that the
atom-attribute will be within a range of values, and every value
within the range is mapped to a specific color. Depending on how the
color map is defined, that mapping can take place via interpolation so
that a value of -3.2 is halfway between “red” and “blue”, or
discretely so that the value of -3.2 is “orange”.</p>
<p>If “vx”, for example, is used as the <em>diameter</em> setting, then the atom
will be rendered using the x-component of its velocity as the
diameter. If the per-atom value <= 0.0, them the atom will not be
drawn. Note that finite-size spherical particles, as defined by
<a class="reference internal" href="atom_style.html"><em>atom_style sphere</em></a> define a per-particle radius or
diameter, which can be used as the <em>diameter</em> setting.</p>
<hr class="docutils" />
<p>The various kewords listed above control how the image is rendered.
As listed below, all of the keywords have defaults, most of which you
will likely not need to change. The <a class="reference internal" href="dump_modify.html"><em>dump modify</em></a>
also has options specific to the dump image style, particularly for
assigning colors to atoms, bonds, and other image features.</p>
<hr class="docutils" />
-<p>The <em>adiam</em> keyword allows you to override the <em>diameter</em> setting to a
-per-atom attribute with a specified numeric value. All atoms will be
-drawn with that diameter, e.g. 1.5, 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>atom</em> keyword allow you to turn off the drawing of all atoms,
-if the specified value is <em>no</em>.</p>
-<p>The <em>body</em> keyword can be used when <a class="reference internal" href="atom_style.html"><em>atom_style body</em></a>
-is used to define body particles with internal state
-(e.g. sub-particles). The <a class="reference internal" href="body.html"><em>body</em></a> doc page descibes the body
-styles LAMMPS currently supports, and provides more details as to the
-kind of body particles they represent and how they are drawn by this
-dump image command. For all the body styles, individual atoms can be
-either a body particle or a usual point (non-body) particle. If the
-<em>body</em> keyword is set to <em>yes</em>, then atoms which are body particles
-are drawn by the method defined by the body style. Non-body particles
-the same way they would be if the <em>body</em> keyword is <em>no</em>, i.e. as
-spheres. The <em>bflag1</em> and <em>bflag2</em> settings are numerical values
-which are passed to the body style to affect how the drawing of a body
-particle is done. See the <a class="reference internal" href="body.html"><em>body</em></a> doc page for a description
-of what these parameters mean for each body style.</p>
+<p>The <em>atom</em> keyword allow you to turn off the drawing of all atoms, if
+the specified value is <em>no</em>. Note that this will not turn off the
+drawing of particles that are represented as lines, triangles, or
+bodies, as discussed below. These particles can be drawn separately
+if the <em>line</em>, <em>tri</em>, or <em>body</em> keywords are used.</p>
+<p>The <em>adiam</em> keyword allows you to override the <em>diameter</em> setting to
+set a single numeric <em>size</em>. All atoms will be drawn with that
+diameter, e.g. 1.5, 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>bond</em> keyword allows to you to alter how bonds are drawn. A bond
is only drawn if both atoms in the bond are being drawn due to being
in the specified group and due to other selection criteria
(e.g. region, threshhold settings of the
<a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a> command). By default, bonds are drawn
if they are defined in the input data file as read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> command. Using <em>none</em> for both the bond
<em>color</em> and <em>width</em> value will turn off the drawing of all bonds.</p>
<p>If <em>atom</em> is specified for the bond <em>color</em> value, then each bond is
drawn in 2 halves, with the color of each half being the color of the
atom at that end of the bond.</p>
<p>If <em>type</em> is specified for the <em>color</em> value, then the color of each
bond is determined by its bond type. By default the mapping of bond
types to colors is as follows:</p>
<ul class="simple">
<li>type 1 = red</li>
<li>type 2 = green</li>
<li>type 3 = blue</li>
<li>type 4 = yellow</li>
<li>type 5 = aqua</li>
<li>type 6 = cyan</li>
</ul>
<p>and repeats itself for bond types > 6. This mapping can be changed by
the <a class="reference internal" href="dump_modify.html"><em>dump_modify bcolor</em></a> command.</p>
<p>The bond <em>width</em> value can be a numeric value or <em>atom</em> or <em>type</em> (or
<em>none</em> as indicated above).</p>
<p>If a numeric value is specified, then all bonds 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>If <em>atom</em> is specified for the <em>width</em> value, then each bond
will be drawn with a width corresponding to the minimum diameter
of the 2 atoms in the bond.</p>
<p>If <em>type</em> is specified for the <em>width</em> value then the diameter of each
bond is determined by its bond type. By default all types have
diameter 0.5. This mapping can be changed by the <a class="reference internal" href="dump_modify.html"><em>dump_modify bdiam</em></a> command.</p>
+<p>The <em>line</em> keyword can be used when <a class="reference internal" href="atom_style.html"><em>atom_style line</em></a>
+is used to define particles as line segments, and will draw them as
+lines. 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 lines 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>
+<li>type 3 = blue</li>
+<li>type 4 = yellow</li>
+<li>type 5 = aqua</li>
+<li>type 6 = cyan</li>
+</ul>
+<p>and repeats itself for types > 6. There is not yet an option to
+change this via the <a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a> command.</p>
+<p>The line <em>width</em> can only be a numeric value, which specifies that all
+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>
+<ul class="simple">
+<li>type 1 = red</li>
+<li>type 2 = green</li>
+<li>type 3 = blue</li>
+<li>type 4 = yellow</li>
+<li>type 5 = aqua</li>
+<li>type 6 = cyan</li>
+</ul>
+<p>and repeats itself for types > 6. There is not yet an option to
+change this via the <a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a> command.</p>
+<p>The <em>body</em> keyword can be used when <a class="reference internal" href="atom_style.html"><em>atom_style body</em></a>
+is used to define body particles with internal state
+(e.g. sub-particles), and will drawn them in a manner specific to the
+body style. If this keyword is not used, such particles will be drawn
+as spheres, the same as if they were regular atoms.</p>
+<p>The <a class="reference internal" href="body.html"><em>body</em></a> doc page descibes the body styles LAMMPS
+currently supports, and provides more details as to the kind of body
+particles they represent and how they are drawn by this dump image
+command. For all the body styles, individual atoms can be either a
+body particle or a usual point (non-body) particle. Non-body
+particles will be drawn the same way they would be as a regular atom.
+The <em>bflag1</em> and <em>bflag2</em> settings are numerical values which are
+passed to the body style to affect how the drawing of a body particle
+is done. See the <a class="reference internal" href="body.html"><em>body</em></a> doc page for a description of what
+these parameters mean for each body style.</p>
<hr class="docutils" />
<p>The <em>size</em> keyword sets the width and height of the created images,
i.e. the number of pixels in each direction.</p>
<hr class="docutils" />
<p>The <em>view</em>, <em>center</em>, <em>up</em>, <em>zoom</em>, and <em>persp</em> values determine how
3d simulation space is mapped to the 2d plane of the image. Basically
they control how the simulation box appears in the image.</p>
<p>All of the <em>view</em>, <em>center</em>, <em>up</em>, <em>zoom</em>, and <em>persp</em> values can be
specified as numeric quantities, whose meaning is explained below.
Any of them can also be specified as an <a class="reference internal" href="variable.html"><em>equal-style variable</em></a>, by using v_name as the value, where “name” is
the variable name. In this case the variable will be evaluated on the
timestep each image is created to create a new value. If the
equal-style variable is time-dependent, this is a means of changing
the way the simulation box appears from image to image, effectively
doing a pan or fly-by view of your simulation.</p>
<p>The <em>view</em> keyword determines the viewpoint from which the simulation
box is viewed, looking towards the <em>center</em> point. The <em>theta</em> value
is the vertical angle from the +z axis, and must be an angle from 0 to
180 degrees. The <em>phi</em> value is an azimuthal angle around the z axis
and can be positive or negative. A value of 0.0 is a view along the
+x axis, towards the <em>center</em> point. If <em>theta</em> or <em>phi</em> are
specified via variables, then the variable values should be in
degrees.</p>
<p>The <em>center</em> keyword determines the point in simulation space that
will be at the center of the image. <em>Cx</em>, <em>Cy</em>, and <em>Cz</em> are
speficied as fractions of the box dimensions, so that (0.5,0.5,0.5) is
the center of the simulation box. These values do not have to be
between 0.0 and 1.0, if you want the simulation box to be offset from
the center of the image. Note, however, that if you choose strange
values for <em>Cx</em>, <em>Cy</em>, or <em>Cz</em> you may get a blank image. Internally,
<em>Cx</em>, <em>Cy</em>, and <em>Cz</em> are converted into a point in simulation space.
If <em>flag</em> is set to “s” for static, then this conversion is done once,
at the time the dump command is issued. If <em>flag</em> is set to “d” for
dynamic then the conversion is performed every time a new image is
created. If the box size or shape is changing, this will adjust the
center point in simulation space.</p>
<p>The <em>up</em> keyword determines what direction in simulation space will be
“up” in the image. Internally it is stored as a vector that is in the
plane perpendicular to the view vector implied by the <em>theta</em> and
<em>pni</em> values, and which is also in the plane defined by the view
vector and user-specified up vector. Thus this internal vector is
computed from the user-specified <em>up</em> vector as</p>
<div class="highlight-python"><div class="highlight"><pre>up_internal = view cross (up cross view)
</pre></div>
</div>
<p>This means the only restriction on the specified <em>up</em> vector is that
it cannot be parallel to the <em>view</em> vector, implied by the <em>theta</em> and
<em>phi</em> values.</p>
<p>The <em>zoom</em> keyword scales the size of the simulation box as it appears
in the image. The default <em>zfactor</em> value of 1 should display an
image mostly filled by the atoms in the simulation box. A <em>zfactor</em> >
1 will make the simulation box larger; a <em>zfactor</em> < 1 will make it
smaller. <em>Zfactor</em> must be a value > 0.0.</p>
<p>The <em>persp</em> keyword determines how much depth perspective is present
in the image. Depth perspective makes lines that are parallel in
simulation space appear non-parallel in the image. A <em>pfactor</em> value
of 0.0 means that parallel lines will meet at infininty (1.0/pfactor),
which is an orthographic rendering with no persepctive. A <em>pfactor</em>
value between 0.0 and 1.0 will introduce more perspective. A <em>pfactor</em>
value > 1 will create a highly skewed image with a large amount of
perspective.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The <em>persp</em> keyword is not yet supported as an option.</p>
</div>
<hr class="docutils" />
<p>The <em>box</em> keyword determines if and how the simulation box boundaries
are rendered as thin cylinders in the image. If <em>no</em> is set, then the
box boundaries are not drawn and the <em>diam</em> setting is ignored. If
<em>yes</em> is set, the 12 edges of the box are drawn, with a diameter that
is a fraction of the shortest box length in x,y,z (for 3d) or x,y (for
2d). The color of the box boundaries can be set with the <a class="reference internal" href="dump_modify.html"><em>dump_modify boxcolor</em></a> command.</p>
<p>The <em>axes</em> keyword determines if and how the coordinate axes are
rendered as thin cylinders in the image. If <em>no</em> is set, then the
axes are not drawn and the <em>length</em> and <em>diam</em> settings are ignored.
If <em>yes</em> is set, 3 thin cylinders are drawn to represent the x,y,z
axes in colors red,green,blue. The origin of these cylinders will be
offset from the lower left corner of the box by 10%. The <em>length</em>
setting determines how long the cylinders will be as a fraction of the
respective box lengths. The <em>diam</em> setting determines their thickness
as a fraction of the shortest box length in x,y,z (for 3d) or x,y (for
2d).</p>
<p>The <em>subbox</em> keyword determines if and how processor sub-domain
boundaries are rendered as thin cylinders in the image. If <em>no</em> is
set (default), then the sub-domain boundaries are not drawn and the
<em>diam</em> setting is ignored. If <em>yes</em> is set, the 12 edges of each
processor sub-domain are drawn, with a diameter that is a fraction of
the shortest box length in x,y,z (for 3d) or x,y (for 2d). The color
of the sub-domain boundaries can be set with the <a class="reference internal" href="dump_modify.html"><em>dump_modify boxcolor</em></a> command.</p>
<hr class="docutils" />
<p>The <em>shiny</em> keyword determines how shiny the objects rendered in the
image will appear. The <em>sfactor</em> value must be a value 0.0 <=
<em>sfactor</em> <= 1.0, where <em>sfactor</em> = 1 is a highly reflective surface
and <em>sfactor</em> = 0 is a rough non-shiny surface.</p>
<p>The <em>ssao</em> keyword turns on/off a screen space ambient occlusion
(SSAO) model for depth shading. If <em>yes</em> is set, then atoms further
away from the viewer are darkened via a randomized process, which is
perceived as depth. The calculation of this effect can increase the
cost of computing the image by roughly 2x. The strength of the effect
can be scaled by the <em>dfactor</em> parameter. If <em>no</em> is set, no depth
shading is performed.</p>
<hr class="docutils" />
<p>A series of JPEG, PNG, or PPM images can be converted into a movie
file and then played as a movie using commonly available tools. Using
dump style <em>movie</em> automates this step and avoids the intermediate
step of writing (many) image snapshot file. But LAMMPS has to be
compiled with -DLAMMPS_FFMPEG and an FFmpeg executable have to be
installed.</p>
<p>To manually convert JPEG, PNG or PPM files into an animated GIF or
MPEG or other movie file you can use:</p>
<ul class="simple">
<li><ol class="first loweralpha">
<li>Use the ImageMagick convert program.</li>
</ol>
</li>
</ul>
<div class="highlight-python"><div class="highlight"><pre>% convert *.jpg foo.gif
% convert -loop 1 *.ppm foo.mpg
</pre></div>
</div>
<p>Animated GIF files from ImageMagick are unoptimized. You can use a
program like gifsicle to optimize and massively shrink them.
MPEG files created by ImageMagick are in MPEG-1 format with rather
inefficient compression and low quality.</p>
<ul class="simple">
<li><ol class="first loweralpha" start="2">
<li>Use QuickTime.</li>
</ol>
</li>
</ul>
<p>Select “Open Image Sequence” under the File menu Load the images into
QuickTime to animate them Select “Export” under the File menu Save the
movie as a QuickTime movie (<a href="#id7"><span class="problematic" id="id8">*</span></a>.mov) or in another format. QuickTime
can generate very high quality and efficiently compressed movie
files. Some of the supported formats require to buy a license and some
are not readable on all platforms until specific runtime libraries are
installed.</p>
<ul class="simple">
<li><ol class="first loweralpha" start="3">
<li>Use FFmpeg</li>
</ol>
</li>
</ul>
<p>FFmpeg is a command line tool that is available on many platforms and
allows extremely flexible encoding and decoding of movies.</p>
<div class="highlight-python"><div class="highlight"><pre>cat snap.*.jpg | ffmpeg -y -f image2pipe -c:v mjpeg -i - -b:v 2000k movie.m4v
cat snap.*.ppm | ffmpeg -y -f image2pipe -c:v ppm -i - -b:v 2400k movie.avi
</pre></div>
</div>
<p>Frontends for FFmpeg exist for multiple platforms. For more
information see the <a class="reference external" href="http://www.ffmpeg.org/">FFmpeg homepage</a></p>
<hr class="docutils" />
<p>Play the movie:</p>
<ul class="simple">
<li><ol class="first loweralpha">
<li>Use your browser to view an animated GIF movie.</li>
</ol>
</li>
</ul>
<p>Select “Open File” under the File menu
Load the animated GIF file</p>
<ul class="simple">
<li>b) Use the freely available mplayer or ffplay tool to view a
movie. Both are available for multiple OSes and support a large
variety of file formats and decoders.</li>
</ul>
<div class="highlight-python"><div class="highlight"><pre>% mplayer foo.mpg
% ffplay bar.avi
</pre></div>
</div>
<ul class="simple">
<li>c) Use the <a class="reference external" href="http://www.sandia.gov/~sjplimp/pizza.html">Pizza.py</a>
<a class="reference external" href="http://www.sandia.gov/~sjplimp/pizza/doc/animate.html">animate tool</a>,
which works directly on a series of image files.</li>
</ul>
<div class="highlight-python"><div class="highlight"><pre><span class="n">a</span> <span class="o">=</span> <span class="n">animate</span><span class="p">(</span><span class="s">"foo*.jpg"</span><span class="p">)</span>
</pre></div>
</div>
<ul class="simple">
<li>d) QuickTime and other Windows- or MacOS-based media players can
obviously play movie files directly. Similarly for corresponding tools
bundled with Linux desktop environments. However, due to licensing
issues with some file formats, the formats may require installing
additional libraries, purchasing a license, or may not be
supported.</li>
</ul>
<hr class="docutils" />
<p>See <a class="reference internal" href="Section_modify.html"><em>Section_modify</em></a> of the manual for information
on how to add new compute and fix styles to LAMMPS to calculate
per-atom quantities which could then be output into dump files.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
<p>To write JPEG images, you must use the -DLAMMPS_JPEG switch when
building LAMMPS and link with a JPEG library. To write PNG images, you
must use the -DLAMMPS_PNG switch when building LAMMPS and link with a
PNG library.</p>
<p>To write <em>movie</em> dumps, you must use the -DLAMMPS_FFMPEG switch when
building LAMMPS and have the FFmpeg executable available on the
machine where LAMMPS is being run. Typically it’s name is lowercase,
i.e. ffmpeg.</p>
<p>See the <a class="reference internal" href="Section_start.html#start-2-4"><span>Making LAMMPS</span></a> section of the
documentation for details on how to compile with optional switches.</p>
<p>Note that since FFmpeg is run as an external program via a pipe,
LAMMPS has limited control over its execution and no knowledge about
errors and warnings printed by it. Those warnings and error messages
will be printed to the screen only. Due to the way image data is
communicated to FFmpeg, it will often print the message</p>
<div class="highlight-python"><div class="highlight"><pre>pipe:: Input/output error
</pre></div>
</div>
<p>which can be safely ignored. Other warnings
and errors have to be addressed according to the FFmpeg documentation.
One known issue is that certain movie file formats (e.g. MPEG level 1
and 2 format streams) have video bandwith limits that can be crossed
when rendering too large of image sizes. Typical warnings look like
this:</p>
<div class="highlight-python"><div class="highlight"><pre>[mpeg @ 0x98b5e0] packet too large, ignoring buffer limits to mux it
[mpeg @ 0x98b5e0] buffer underflow st=0 bufi=281407 size=285018
[mpeg @ 0x98b5e0] buffer underflow st=0 bufi=283448 size=285018
</pre></div>
</div>
<p>In this case it is recommended to either reduce the size of the image
or encode in a different format that is also supported by your copy of
FFmpeg, and which does not have this limitation (e.g. .avi, .mkv,
mp4).</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
<p><a class="reference internal" href="dump.html"><em>dump</em></a>, <a class="reference internal" href="dump_modify.html"><em>dump_modify</em></a>, <a class="reference internal" href="undump.html"><em>undump</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
<p>The defaults for the keywords are as follows:</p>
<ul class="simple">
<li>adiam = not specified (use diameter setting)</li>
<li>atom = yes</li>
<li>bond = none none (if no bonds in system)</li>
<li>bond = atom 0.5 (if bonds in system)</li>
<li>size = 512 512</li>
<li>view = 60 30 (for 3d)</li>
<li>view = 0 0 (for 2d)</li>
<li>center = s 0.5 0.5 0.5</li>
<li>up = 0 0 1 (for 3d)</li>
<li>up = 0 1 0 (for 2d)</li>
<li>zoom = 1.0</li>
<li>persp = 0.0</li>
<li>box = yes 0.02</li>
<li>axes = no 0.0 0.0</li>
<li>subbox no 0.0</li>
<li>shiny = 1.0</li>
<li>ssao = no</li>
</ul>
</div>
</div>
</div>
</div>
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diff --git a/doc/dump_image.txt b/doc/dump_image.txt
index f671e747d..497bc46d7 100644
--- a/doc/dump_image.txt
+++ b/doc/dump_image.txt
@@ -1,568 +1,619 @@
"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
dump image command :h3
dump movie command :h3
[Syntax:]
dump ID group-ID style N file color diameter keyword value ... :pre
ID = user-assigned name for the dump :ulb,l
group-ID = ID of the group of atoms to be imaged :l
style = {image} or {movie} = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) :l
N = dump every this many timesteps :l
file = name of file to write image to :l
color = atom attribute that determines color of each atom :l
diameter = atom attribute that determines size of each atom :l
zero or more keyword/value pairs may be appended :l
-keyword = {adiam} or {atom} or {body} or {bond} or {size} or {view} or {center} or {up} or {zoom} or {persp} or {box} or {axes} or {subbox} or {shiny} or {ssao} :l
- {adiam} value = number = numeric value for atom diameter (distance units)
+keyword = {atom} or {adiam} or {bond} or {line} or {tri} or {body} or {size} or {view} or {center} or {up} or {zoom} or {persp} or {box} or {axes} or {subbox} or {shiny} or {ssao} :l
{atom} = yes/no = do or do not draw atoms
- {body} = yes/no bflag1 bflag2
- yes/no = do or do not draw atoms as bodies
- bflag1,bflag2 = 2 numeric flags to affect how bodies are drawn
+ {adiam} size = numeric value for atom diameter (distance units)
{bond} values = color width = color and width of bonds
color = {atom} or {type} or {none}
width = number or {atom} or {type} or {none}
number = numeric value for bond width (distance units)
+ {line} = color width
+ color = {type}
+ width = numeric value for line width (distance units)
+ {tri} = color
+ color = {type}
+ {body} = color bflag1 bflag2
+ color = {type}
+ bflag1,bflag2 = 2 numeric flags to affect how bodies are drawn
{size} values = width height = size of images
width = width of image in # of pixels
height = height of image in # of pixels
{view} values = theta phi = view of simulation box
theta = view angle from +z axis (degrees)
phi = azimuthal view angle (degrees)
theta or phi can be a variable (see below)
{center} values = flag Cx Cy Cz = center point of image
flag = "s" for static, "d" for dynamic
Cx,Cy,Cz = center point of image as fraction of box dimension (0.5 = center of box)
Cx,Cy,Cz can be variables (see below)
{up} values = Ux Uy Uz = direction that is "up" in image
Ux,Uy,Uz = components of up vector
Ux,Uy,Uz can be variables (see below)
{zoom} value = zfactor = size that simulation box appears in image
zfactor = scale image size by factor > 1 to enlarge, factor < 1 to shrink
zfactor can be a variable (see below)
{persp} value = pfactor = amount of "perspective" in image
pfactor = amount of perspective (0 = none, < 1 = some, > 1 = highly skewed)
pfactor can be a variable (see below)
{box} values = yes/no diam = draw outline of simulation box
yes/no = do or do not draw simulation box lines
diam = diameter of box lines as fraction of shortest box length
{axes} values = yes/no length diam = draw xyz axes
yes/no = do or do not draw xyz axes lines next to simulation box
length = length of axes lines as fraction of respective box lengths
diam = diameter of axes lines as fraction of shortest box length
{subbox} values = yes/no diam = draw outline of processor sub-domains
yes/no = do or do not draw sub-domain lines
diam = diameter of sub-domain lines as fraction of shortest box length
{shiny} value = sfactor = shinyness of spheres and cylinders
sfactor = shinyness of spheres and cylinders from 0.0 to 1.0
{ssao} value = yes/no seed dfactor = SSAO depth shading
yes/no = turn depth shading on/off
seed = random # seed (positive integer)
dfactor = strength of shading from 0.0 to 1.0 :pre
:ule
[Examples:]
dump d0 all image 100 dump.*.jpg type type
dump d1 mobile image 500 snap.*.png element element ssao yes 4539 0.6
dump d2 all image 200 img-*.ppm type type zoom 2.5 adiam 1.5 size 1280 720
dump m0 all movie 1000 movie.mpg type type size 640 480
dump m1 all movie 1000 movie.avi type type size 640 480
dump m2 all movie 100 movie.m4v type type zoom 1.8 adiam v_value size 1280 720 :pre
[Description:]
Dump a high-quality rendered image of the atom configuration every N
timesteps and save the images either as a sequence of JPEG or PNG or
PPM files, or as a single movie file. The options for this command as
well as the "dump_modify"_dump_modify.html command control what is
included in the image or movie and how it appears. A series of such
images can easily be manually converted into an animated movie of your
simulation or the process can be automated without writing the
intermediate files using the dump movie style; see further details
below. Other dump styles store snapshots of numerical data asociated
with atoms in various formats, as discussed on the "dump"_dump.html
doc page.
Note that a set of images or a movie can be made after a simulation
has been run, using the "rerun"_rerun.html command to read snapshots
from an existing dump file, and using these dump commands in the rerun
script to generate the images/movie.
Here are two sample images, rendered as 1024x1024 JPEG files. Click
to see the full-size images:
<DIV ALIGN=center>
:image(JPG/dump1_small.jpg,JPG/dump1.jpg)
:image(JPG/dump2_small.jpg,JPG/dump2.jpg)
</DIV>
Only atoms in the specified group are rendered in the image. The
"dump_modify region and thresh"_dump_modify.html commands can also
alter what atoms are included in the image.\
The filename suffix determines whether a JPEG, PNG, or PPM file is
created with the {image} dump style. If the suffix is ".jpg" or
".jpeg", then a JPEG format file is created, if the suffix is ".png",
then a PNG format is created, else a PPM (aka NETPBM) format file is
created. The JPEG and PNG files are binary; PPM has a text mode
header followed by binary data. JPEG images have lossy compression;
PNG has lossless compression; and PPM files are uncompressed but can
be compressed with gzip, if LAMMPS has been compiled with
-DLAMMPS_GZIP and a ".gz" suffix is used.
Similarly, the format of the resulting movie is chosen with the
{movie} dump style. This is handled by the underlying FFmpeg converter
and thus details have to be looked up in the FFmpeg documentation.
Typical examples are: .avi, .mpg, .m4v, .mp4, .mkv, .flv, .mov, .gif
Additional settings of the movie compression like bitrate and
framerate can be set using the "dump_modify"_dump_modify.html command.
To write out JPEG and PNG format files, you must build LAMMPS with
support for the corresponding JPEG or PNG library. To convert images
into movies, LAMMPS has to be compiled with the -DLAMMPS_FFMPEG
flag. See "this section"_Section_start.html#start_2_4 of the manual
for instructions on how to do this.
NOTE: Because periodic boundary conditions are enforced only on
timesteps when neighbor lists are rebuilt, the coordinates of an atom
in the image may be slightly outside the simulation box.
:line
Dumps are performed on timesteps that are a multiple of N (including
timestep 0) and on the last timestep of a minimization if the
minimization converges. Note that this means a dump will not be
performed on the initial timestep after the dump command is invoked,
if the current timestep is not a multiple of N. This behavior can be
changed via the "dump_modify first"_dump_modify.html command, which
can be useful if the dump command is invoked after a minimization
ended on an arbitrary timestep. N can be changed between runs by
using the "dump_modify every"_dump_modify.html command.
Dump {image} filenames must contain a wildcard character "*", so that
one image file per snapshot is written. The "*" character is replaced
with the timestep value. For example, tmp.dump.*.jpg becomes
tmp.dump.0.jpg, tmp.dump.10000.jpg, tmp.dump.20000.jpg, etc. Note
that the "dump_modify pad"_dump_modify.html command can be used to
insure all timestep numbers are the same length (e.g. 00010), which
can make it easier to convert a series of images into a movie in the
correct ordering.
Dump {movie} filenames on the other hand, must not have any wildcard
character since only one file combining all images into a single
movie will be written by the movie encoder.
:line
The {color} and {diameter} settings determine the color and size of
atoms rendered in the image. They can be any atom attribute defined
for the "dump custom"_dump.html command, including {type} and
{element}. This includes per-atom quantities calculated by a
"compute"_compute.html, "fix"_fix.html, or "variable"_variable.html,
which are prefixed by "c_", "f_", or "v_" respectively. Note that the
{diameter} setting can be overridden with a numeric value applied to
all atoms by the optional {adiam} keyword.
If {type} is specified for the {color} setting, then the color of each
atom is determined by its atom type. By default the mapping of types
to colors is as follows:
type 1 = red
type 2 = green
type 3 = blue
type 4 = yellow
type 5 = aqua
type 6 = cyan :ul
and repeats itself for types > 6. This mapping can be changed by the
"dump_modify acolor"_dump_modify.html command.
If {type} is specified for the {diameter} setting then the diameter of
each atom is determined by its atom type. By default all types have
diameter 1.0. This mapping can be changed by the "dump_modify
adiam"_dump_modify.html command.
If {element} is specified for the {color} and/or {diameter} setting,
then the color and/or diameter of each atom is determined by which
element it is, which in turn is specified by the element-to-type
mapping specified by the "dump_modify element" command. By default
every atom type is C (carbon). Every element has a color and diameter
associated with it, which is the same as the colors and sizes used by
the "AtomEye"_atomeye visualization package.
:link(atomeye,http://mt.seas.upenn.edu/Archive/Graphics/A)
If other atom attributes are used for the {color} or {diameter}
settings, they are interpreted in the following way.
If "vx", for example, is used as the {color} setting, then the color
of the atom will depend on the x-component of its velocity. The
association of a per-atom value with a specific color is determined by
a "color map", which can be specified via the
"dump_modify"_dump_modify.html command. The basic idea is that the
atom-attribute will be within a range of values, and every value
within the range is mapped to a specific color. Depending on how the
color map is defined, that mapping can take place via interpolation so
that a value of -3.2 is halfway between "red" and "blue", or
discretely so that the value of -3.2 is "orange".
If "vx", for example, is used as the {diameter} setting, then the atom
will be rendered using the x-component of its velocity as the
diameter. If the per-atom value <= 0.0, them the atom will not be
drawn. Note that finite-size spherical particles, as defined by
"atom_style sphere"_atom_style.html define a per-particle radius or
diameter, which can be used as the {diameter} setting.
:line
The various kewords listed above control how the image is rendered.
As listed below, all of the keywords have defaults, most of which you
will likely not need to change. The "dump modify"_dump_modify.html
also has options specific to the dump image style, particularly for
assigning colors to atoms, bonds, and other image features.
:line
-The {adiam} keyword allows you to override the {diameter} setting to a
-per-atom attribute with a specified numeric value. All atoms will be
-drawn with that diameter, e.g. 1.5, which is in whatever distance
-"units"_units.html the input script defines, e.g. Angstroms.
+The {atom} keyword allow you to turn off the drawing of all atoms, if
+the specified value is {no}. Note that this will not turn off the
+drawing of particles that are represented as lines, triangles, or
+bodies, as discussed below. These particles can be drawn separately
+if the {line}, {tri}, or {body} keywords are used.
-The {atom} keyword allow you to turn off the drawing of all atoms,
-if the specified value is {no}.
-
-The {body} keyword can be used when "atom_style body"_atom_style.html
-is used to define body particles with internal state
-(e.g. sub-particles). The "body"_body.html doc page descibes the body
-styles LAMMPS currently supports, and provides more details as to the
-kind of body particles they represent and how they are drawn by this
-dump image command. For all the body styles, individual atoms can be
-either a body particle or a usual point (non-body) particle. If the
-{body} keyword is set to {yes}, then atoms which are body particles
-are drawn by the method defined by the body style. Non-body particles
-the same way they would be if the {body} keyword is {no}, i.e. as
-spheres. The {bflag1} and {bflag2} settings are numerical values
-which are passed to the body style to affect how the drawing of a body
-particle is done. See the "body"_body.html doc page for a description
-of what these parameters mean for each body style.
+The {adiam} keyword allows you to override the {diameter} setting to
+set a single numeric {size}. All atoms will be drawn with that
+diameter, e.g. 1.5, which is in whatever distance "units"_units.html
+the input script defines, e.g. Angstroms.
The {bond} keyword allows to you to alter how bonds are drawn. A bond
is only drawn if both atoms in the bond are being drawn due to being
in the specified group and due to other selection criteria
(e.g. region, threshhold settings of the
"dump_modify"_dump_modify.html command). By default, bonds are drawn
if they are defined in the input data file as read by the
"read_data"_read_data.html command. Using {none} for both the bond
{color} and {width} value will turn off the drawing of all bonds.
If {atom} is specified for the bond {color} value, then each bond is
drawn in 2 halves, with the color of each half being the color of the
atom at that end of the bond.
If {type} is specified for the {color} value, then the color of each
bond is determined by its bond type. By default the mapping of bond
types to colors is as follows:
type 1 = red
type 2 = green
type 3 = blue
type 4 = yellow
type 5 = aqua
type 6 = cyan :ul
and repeats itself for bond types > 6. This mapping can be changed by
the "dump_modify bcolor"_dump_modify.html command.
The bond {width} value can be a numeric value or {atom} or {type} (or
{none} as indicated above).
If a numeric value is specified, then all bonds will be drawn as
cylinders with that diameter, e.g. 1.0, which is in whatever distance
"units"_units.html the input script defines, e.g. Angstroms.
If {atom} is specified for the {width} value, then each bond
will be drawn with a width corresponding to the minimum diameter
of the 2 atoms in the bond.
If {type} is specified for the {width} value then the diameter of each
bond is determined by its bond type. By default all types have
diameter 0.5. This mapping can be changed by the "dump_modify
bdiam"_dump_modify.html command.
+The {line} keyword can be used when "atom_style line"_atom_style.html
+is used to define particles as line segments, and will draw them as
+lines. 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 lines 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
+type 3 = blue
+type 4 = yellow
+type 5 = aqua
+type 6 = cyan :ul
+
+and repeats itself for types > 6. There is not yet an option to
+change this via the "dump_modify"_dump_modify.html command.
+
+The line {width} can only be a numeric value, which specifies that all
+lines will be drawn as cylinders with that diameter, e.g. 1.0, which
+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:
+
+type 1 = red
+type 2 = green
+type 3 = blue
+type 4 = yellow
+type 5 = aqua
+type 6 = cyan :ul
+
+and repeats itself for types > 6. There is not yet an option to
+change this via the "dump_modify"_dump_modify.html command.
+
+The {body} keyword can be used when "atom_style body"_atom_style.html
+is used to define body particles with internal state
+(e.g. sub-particles), and will drawn them in a manner specific to the
+body style. If this keyword is not used, such particles will be drawn
+as spheres, the same as if they were regular atoms.
+
+The "body"_body.html doc page descibes the body styles LAMMPS
+currently supports, and provides more details as to the kind of body
+particles they represent and how they are drawn by this dump image
+command. For all the body styles, individual atoms can be either a
+body particle or a usual point (non-body) particle. Non-body
+particles will be drawn the same way they would be as a regular atom.
+The {bflag1} and {bflag2} settings are numerical values which are
+passed to the body style to affect how the drawing of a body particle
+is done. See the "body"_body.html doc page for a description of what
+these parameters mean for each body style.
+
:line
The {size} keyword sets the width and height of the created images,
i.e. the number of pixels in each direction.
:line
The {view}, {center}, {up}, {zoom}, and {persp} values determine how
3d simulation space is mapped to the 2d plane of the image. Basically
they control how the simulation box appears in the image.
All of the {view}, {center}, {up}, {zoom}, and {persp} values can be
specified as numeric quantities, whose meaning is explained below.
Any of them can also be specified as an "equal-style
variable"_variable.html, by using v_name as the value, where "name" is
the variable name. In this case the variable will be evaluated on the
timestep each image is created to create a new value. If the
equal-style variable is time-dependent, this is a means of changing
the way the simulation box appears from image to image, effectively
doing a pan or fly-by view of your simulation.
The {view} keyword determines the viewpoint from which the simulation
box is viewed, looking towards the {center} point. The {theta} value
is the vertical angle from the +z axis, and must be an angle from 0 to
180 degrees. The {phi} value is an azimuthal angle around the z axis
and can be positive or negative. A value of 0.0 is a view along the
+x axis, towards the {center} point. If {theta} or {phi} are
specified via variables, then the variable values should be in
degrees.
The {center} keyword determines the point in simulation space that
will be at the center of the image. {Cx}, {Cy}, and {Cz} are
speficied as fractions of the box dimensions, so that (0.5,0.5,0.5) is
the center of the simulation box. These values do not have to be
between 0.0 and 1.0, if you want the simulation box to be offset from
the center of the image. Note, however, that if you choose strange
values for {Cx}, {Cy}, or {Cz} you may get a blank image. Internally,
{Cx}, {Cy}, and {Cz} are converted into a point in simulation space.
If {flag} is set to "s" for static, then this conversion is done once,
at the time the dump command is issued. If {flag} is set to "d" for
dynamic then the conversion is performed every time a new image is
created. If the box size or shape is changing, this will adjust the
center point in simulation space.
The {up} keyword determines what direction in simulation space will be
"up" in the image. Internally it is stored as a vector that is in the
plane perpendicular to the view vector implied by the {theta} and
{pni} values, and which is also in the plane defined by the view
vector and user-specified up vector. Thus this internal vector is
computed from the user-specified {up} vector as
up_internal = view cross (up cross view) :pre
This means the only restriction on the specified {up} vector is that
it cannot be parallel to the {view} vector, implied by the {theta} and
{phi} values.
The {zoom} keyword scales the size of the simulation box as it appears
in the image. The default {zfactor} value of 1 should display an
image mostly filled by the atoms in the simulation box. A {zfactor} >
1 will make the simulation box larger; a {zfactor} < 1 will make it
smaller. {Zfactor} must be a value > 0.0.
The {persp} keyword determines how much depth perspective is present
in the image. Depth perspective makes lines that are parallel in
simulation space appear non-parallel in the image. A {pfactor} value
of 0.0 means that parallel lines will meet at infininty (1.0/pfactor),
which is an orthographic rendering with no persepctive. A {pfactor}
value between 0.0 and 1.0 will introduce more perspective. A {pfactor}
value > 1 will create a highly skewed image with a large amount of
perspective.
NOTE: The {persp} keyword is not yet supported as an option.
:line
The {box} keyword determines if and how the simulation box boundaries
are rendered as thin cylinders in the image. If {no} is set, then the
box boundaries are not drawn and the {diam} setting is ignored. If
{yes} is set, the 12 edges of the box are drawn, with a diameter that
is a fraction of the shortest box length in x,y,z (for 3d) or x,y (for
2d). The color of the box boundaries can be set with the "dump_modify
boxcolor"_dump_modify.html command.
The {axes} keyword determines if and how the coordinate axes are
rendered as thin cylinders in the image. If {no} is set, then the
axes are not drawn and the {length} and {diam} settings are ignored.
If {yes} is set, 3 thin cylinders are drawn to represent the x,y,z
axes in colors red,green,blue. The origin of these cylinders will be
offset from the lower left corner of the box by 10%. The {length}
setting determines how long the cylinders will be as a fraction of the
respective box lengths. The {diam} setting determines their thickness
as a fraction of the shortest box length in x,y,z (for 3d) or x,y (for
2d).
The {subbox} keyword determines if and how processor sub-domain
boundaries are rendered as thin cylinders in the image. If {no} is
set (default), then the sub-domain boundaries are not drawn and the
{diam} setting is ignored. If {yes} is set, the 12 edges of each
processor sub-domain are drawn, with a diameter that is a fraction of
the shortest box length in x,y,z (for 3d) or x,y (for 2d). The color
of the sub-domain boundaries can be set with the "dump_modify
boxcolor"_dump_modify.html command.
:line
The {shiny} keyword determines how shiny the objects rendered in the
image will appear. The {sfactor} value must be a value 0.0 <=
{sfactor} <= 1.0, where {sfactor} = 1 is a highly reflective surface
and {sfactor} = 0 is a rough non-shiny surface.
The {ssao} keyword turns on/off a screen space ambient occlusion
(SSAO) model for depth shading. If {yes} is set, then atoms further
away from the viewer are darkened via a randomized process, which is
perceived as depth. The calculation of this effect can increase the
cost of computing the image by roughly 2x. The strength of the effect
can be scaled by the {dfactor} parameter. If {no} is set, no depth
shading is performed.
:line
A series of JPEG, PNG, or PPM images can be converted into a movie
file and then played as a movie using commonly available tools. Using
dump style {movie} automates this step and avoids the intermediate
step of writing (many) image snapshot file. But LAMMPS has to be
compiled with -DLAMMPS_FFMPEG and an FFmpeg executable have to be
installed.
To manually convert JPEG, PNG or PPM files into an animated GIF or
MPEG or other movie file you can use:
a) Use the ImageMagick convert program. :ulb,l
% convert *.jpg foo.gif
% convert -loop 1 *.ppm foo.mpg :pre
Animated GIF files from ImageMagick are unoptimized. You can use a
program like gifsicle to optimize and massively shrink them.
MPEG files created by ImageMagick are in MPEG-1 format with rather
inefficient compression and low quality.
b) Use QuickTime. :l
Select "Open Image Sequence" under the File menu Load the images into
QuickTime to animate them Select "Export" under the File menu Save the
movie as a QuickTime movie (*.mov) or in another format. QuickTime
can generate very high quality and efficiently compressed movie
files. Some of the supported formats require to buy a license and some
are not readable on all platforms until specific runtime libraries are
installed.
c) Use FFmpeg :l
FFmpeg is a command line tool that is available on many platforms and
allows extremely flexible encoding and decoding of movies.
cat snap.*.jpg | ffmpeg -y -f image2pipe -c:v mjpeg -i - -b:v 2000k movie.m4v
cat snap.*.ppm | ffmpeg -y -f image2pipe -c:v ppm -i - -b:v 2400k movie.avi :pre
Frontends for FFmpeg exist for multiple platforms. For more
information see the "FFmpeg homepage"_http://www.ffmpeg.org/
:ule
:line
Play the movie:
a) Use your browser to view an animated GIF movie. :ulb,l
Select "Open File" under the File menu
Load the animated GIF file
b) Use the freely available mplayer or ffplay tool to view a
movie. Both are available for multiple OSes and support a large
variety of file formats and decoders. :l
% mplayer foo.mpg
% ffplay bar.avi :pre
c) Use the "Pizza.py"_http://www.sandia.gov/~sjplimp/pizza.html
"animate tool"_http://www.sandia.gov/~sjplimp/pizza/doc/animate.html,
which works directly on a series of image files. :l
a = animate("foo*.jpg") :pre
d) QuickTime and other Windows- or MacOS-based media players can
obviously play movie files directly. Similarly for corresponding tools
bundled with Linux desktop environments. However, due to licensing
issues with some file formats, the formats may require installing
additional libraries, purchasing a license, or may not be
supported. :ule,l
:line
See "Section_modify"_Section_modify.html of the manual for information
on how to add new compute and fix styles to LAMMPS to calculate
per-atom quantities which could then be output into dump files.
:line
[Restrictions:]
To write JPEG images, you must use the -DLAMMPS_JPEG switch when
building LAMMPS and link with a JPEG library. To write PNG images, you
must use the -DLAMMPS_PNG switch when building LAMMPS and link with a
PNG library.
To write {movie} dumps, you must use the -DLAMMPS_FFMPEG switch when
building LAMMPS and have the FFmpeg executable available on the
machine where LAMMPS is being run. Typically it's name is lowercase,
i.e. ffmpeg.
See the "Making LAMMPS"_Section_start.html#start_2_4 section of the
documentation for details on how to compile with optional switches.
Note that since FFmpeg is run as an external program via a pipe,
LAMMPS has limited control over its execution and no knowledge about
errors and warnings printed by it. Those warnings and error messages
will be printed to the screen only. Due to the way image data is
communicated to FFmpeg, it will often print the message
pipe:: Input/output error :pre
which can be safely ignored. Other warnings
and errors have to be addressed according to the FFmpeg documentation.
One known issue is that certain movie file formats (e.g. MPEG level 1
and 2 format streams) have video bandwith limits that can be crossed
when rendering too large of image sizes. Typical warnings look like
this:
\[mpeg @ 0x98b5e0\] packet too large, ignoring buffer limits to mux it
\[mpeg @ 0x98b5e0\] buffer underflow st=0 bufi=281407 size=285018
\[mpeg @ 0x98b5e0\] buffer underflow st=0 bufi=283448 size=285018 :pre
In this case it is recommended to either reduce the size of the image
or encode in a different format that is also supported by your copy of
FFmpeg, and which does not have this limitation (e.g. .avi, .mkv,
mp4).
[Related commands:]
"dump"_dump.html, "dump_modify"_dump_modify.html, "undump"_undump.html
[Default:]
The defaults for the keywords are as follows:
adiam = not specified (use diameter setting)
atom = yes
bond = none none (if no bonds in system)
bond = atom 0.5 (if bonds in system)
size = 512 512
view = 60 30 (for 3d)
view = 0 0 (for 2d)
center = s 0.5 0.5 0.5
up = 0 0 1 (for 3d)
up = 0 1 0 (for 2d)
zoom = 1.0
persp = 0.0
box = yes 0.02
axes = no 0.0 0.0
subbox no 0.0
shiny = 1.0
ssao = no :ul
diff --git a/doc/fix_move.html b/doc/fix_move.html
index 2b0efcda0..337955c92 100644
--- a/doc/fix_move.html
+++ b/doc/fix_move.html
@@ -1,407 +1,408 @@
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<div class="section" id="fix-move-command">
<span id="index-0"></span><h1>fix move command<a class="headerlink" href="#fix-move-command" title="Permalink to this headline">¶</a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
<div class="highlight-python"><div class="highlight"><pre>fix ID group-ID move style args keyword values ...
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><em>fix</em></a> command</li>
<li>move = style name of this fix command</li>
<li>style = <em>linear</em> or <em>wiggle</em> or <em>rotate</em> or <em>variable</em></li>
</ul>
<pre class="literal-block">
<em>linear</em> args = Vx Vy Vz
Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL
<em>wiggle</em> args = Ax Ay Az period
Ax,Ay,Az = components of amplitude vector (distance units), any component can be specified as NULL
period = period of oscillation (time units)
<em>rotate</em> args = Px Py Pz Rx Ry Rz period
Px,Py,Pz = origin point of axis of rotation (distance units)
Rx,Ry,Rz = axis of rotation vector
period = period of rotation (time units)
<em>variable</em> args = v_dx v_dy v_dz v_vx v_vy v_vz
v_dx,v_dy,v_dz = 3 variable names that calculate x,y,z displacement as function of time, any component can be specified as NULL
v_vx,v_vy,v_vz = 3 variable names that calculate x,y,z velocity as function of time, any component can be specified as NULL
</pre>
<ul class="simple">
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>units</em></li>
</ul>
<pre class="literal-block">
<em>units</em> value = <em>box</em> or <em>lattice</em>
</pre>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
<div class="highlight-python"><div class="highlight"><pre>fix 1 boundary move wiggle 3.0 0.0 0.0 1.0 units box
fix 2 boundary move rotate 0.0 0.0 0.0 0.0 0.0 1.0 5.0
fix 2 boundary move variable v_myx v_myy NULL v_VX v_VY NULL
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>Perform updates of position and velocity for atoms in the group each
timestep using the specified settings or formulas, without regard to
forces on the atoms. This can be useful for boundary or other atoms,
whose movement can influence nearby atoms.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The atoms affected by this fix should not normally be time
integrated by other fixes (e.g. <a class="reference internal" href="fix_nve.html"><em>fix nve</em></a>, <a class="reference internal" href="fix_nh.html"><em>fix nvt</em></a>), since that will change their positions and
velocities twice.</p>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">As atoms move due to this fix, they will pass thru periodic
boundaries and be remapped to the other side of the simulation box,
just as they would during normal time integration (e.g. via the <a class="reference internal" href="fix_nve.html"><em>fix nve</em></a> command). It is up to you to decide whether
periodic boundaries are appropriate with the kind of atom motion you
are prescribing with this fix.</p>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">As dicsussed below, atoms are moved relative to their initial
position at the time the fix is specified. These initial coordinates
are stored by the fix in “unwrapped” form, by using the image flags
associated with each atom. See the <a class="reference internal" href="dump.html"><em>dump custom</em></a> command
for a discussion of “unwrapped” coordinates. See the Atoms section of
the <a class="reference internal" href="read_data.html"><em>read_data</em></a> command for a discussion of image flags
and how they are set for each atom. You can reset the image flags
(e.g. to 0) before invoking this fix by using the <a class="reference internal" href="set.html"><em>set image</em></a>
command.</p>
</div>
<hr class="docutils" />
<p>The <em>linear</em> style moves atoms at a constant velocity, so that their
position <em>X</em> = (x,y,z) as a function of time is given in vector
notation as</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">X</span><span class="p">(</span><span class="n">t</span><span class="p">)</span> <span class="o">=</span> <span class="n">X0</span> <span class="o">+</span> <span class="n">V</span> <span class="o">*</span> <span class="n">delta</span>
</pre></div>
</div>
<p>where <em>X0</em> = (x0,y0,z0) is their position at the time the fix is
specified, <em>V</em> is the specified velocity vector with components
(Vx,Vy,Vz), and <em>delta</em> is the time elapsed since the fix was
specified. This style also sets the velocity of each atom to V =
(Vx,Vy,Vz). If any of the velocity components is specified as NULL,
then the position and velocity of that component is time integrated
the same as the <a class="reference internal" href="fix_nve.html"><em>fix nve</em></a> command would perform, using
the corresponding force component on the atom.</p>
<p>Note that the <em>linear</em> style is identical to using the <em>variable</em>
style with an <a class="reference internal" href="variable.html"><em>equal-style variable</em></a> that uses the
vdisplace() function. E.g.</p>
<div class="highlight-python"><div class="highlight"><pre>variable V equal 10.0
variable x equal vdisplace(0.0,$V)
fix 1 boundary move variable v_x NULL NULL v_V NULL NULL
</pre></div>
</div>
<p>The <em>wiggle</em> style moves atoms in an oscillatory fashion, so that
their position <em>X</em> = (x,y,z) as a function of time is given in vector
notation as</p>
<div class="highlight-python"><div class="highlight"><pre>X(t) = X0 + A sin(omega*delta)
</pre></div>
</div>
<p>where <em>X0</em> = (x0,y0,z0) is their position at the time the fix is
specified, <em>A</em> is the specified amplitude vector with components
(Ax,Ay,Az), <em>omega</em> is 2 PI / <em>period</em>, and <em>delta</em> is the time
elapsed since the fix was specified. This style also sets the
velocity of each atom to the time derivative of this expression. If
any of the amplitude components is specified as NULL, then the
position and velocity of that component is time integrated the same as
the <a class="reference internal" href="fix_nve.html"><em>fix nve</em></a> command would perform, using the
corresponding force component on the atom.</p>
<p>Note that the <em>wiggle</em> style is identical to using the <em>variable</em>
style with <a class="reference internal" href="variable.html"><em>equal-style variables</em></a> that use the
swiggle() and cwiggle() functions. E.g.</p>
<div class="highlight-python"><div class="highlight"><pre>variable A equal 10.0
variable T equal 5.0
variable omega equal 2.0*PI/$T
variable x equal swiggle(0.0,$A,$T)
variable v equal v_omega*($A-cwiggle(0.0,$A,$T))
fix 1 boundary move variable v_x NULL NULL v_v NULL NULL
</pre></div>
</div>
<p>The <em>rotate</em> style rotates atoms around a rotation axis <em>R</em> =
(Rx,Ry,Rz) that goes thru a point <em>P</em> = (Px,Py,Pz). The <em>period</em> of
-the rotation is also specified. This style also sets the velocity of
-each atom to (omega cross Rperp) where omega is its angular velocity
-around the rotation axis and Rperp is a perpendicular vector from the
-rotation axis to the atom. If the defined
-<a class="reference internal" href="atom_style.html"><em>atom_style</em></a> assigns an angular velocity to each atom,
-then each atom’s angular velocity is also set to omega. Note that the
-direction of rotation for the atoms around the rotation axis is
-consistent with the right-hand rule: if your right-hand’s thumb points
-along <em>R</em>, then your fingers wrap around the axis in the direction of
-rotation.</p>
+the rotation is also specified. The direction of rotation for the
+atoms around the rotation axis is consistent with the right-hand rule:
+if your right-hand thumb points along <em>R</em>, then your fingers wrap
+around the axis in the direction of rotation.</p>
+<p>This style also sets the velocity of each atom to (omega cross Rperp)
+where omega is its angular velocity around the rotation axis and Rperp
+is a perpendicular vector from the rotation axis to the atom. If the
+defined <a class="reference internal" href="atom_style.html"><em>atom_style</em></a> assigns an angular velocity or
+angular moementum or orientation to each atom (<a class="reference internal" href="atom_style.html"><em>atom styles</em></a> sphere, ellipsoid, line, tri, body), then
+those properties are also updated appropriately to correspond to the
+atom’s motion and rotation over time.</p>
<p>The <em>variable</em> style allows the position and velocity components of
each atom to be set by formulas specified via the
<a class="reference internal" href="variable.html"><em>variable</em></a> command. Each of the 6 variables is
specified as an argument to the fix as v_name, where name is the
variable name that is defined elsewhere in the input script.</p>
<p>Each variable must be of either the <em>equal</em> or <em>atom</em> style.
<em>Equal</em>-style variables compute a single numeric quantity, that can be
a function of the timestep as well as of other simulation values.
<em>Atom</em>-style variables compute a numeric quantity for each atom, that
can be a function per-atom quantities, such as the atom’s position, as
well as of the timestep and other simulation values. Note that this
fix stores the original coordinates of each atom (see note below) so
that per-atom quantity can be used in an atom-style variable formula.
See the <a class="reference internal" href="variable.html"><em>variable</em></a> command for details.</p>
<p>The first 3 variables (v_dx,v_dy,v_dz) specified for the <em>variable</em>
style are used to calculate a displacement from the atom’s original
position at the time the fix was specified. The second 3 variables
(v_vx,v_vy,v_vz) specified are used to compute a velocity for each
atom.</p>
<p>Any of the 6 variables can be specified as NULL. If both the
displacement and velocity variables for a particular x,y,z component
are specified as NULL, then the position and velocity of that
component is time integrated the same as the <a class="reference internal" href="fix_nve.html"><em>fix nve</em></a>
command would perform, using the corresponding force component on the
atom. If only the velocity variable for a component is specified as
NULL, then the displacement variable will be used to set the position
of the atom, and its velocity component will not be changed. If only
the displacement variable for a component is specified as NULL, then
the velocity variable will be used to set the velocity of the atom,
and the position of the atom will be time integrated using that
velocity.</p>
<p>The <em>units</em> keyword determines the meaning of the distance units used
to define the <em>linear</em> velocity and <em>wiggle</em> amplitude and <em>rotate</em>
origin. This setting is ignored for the <em>variable</em> style. A <em>box</em>
value selects standard units as defined by the <a class="reference internal" href="units.html"><em>units</em></a>
command, e.g. velocity in Angstroms/fmsec and amplitude and position
in Angstroms for units = real. A <em>lattice</em> value means the velocity
units are in lattice spacings per time and the amplitude and position
are in lattice spacings. The <a class="reference internal" href="lattice.html"><em>lattice</em></a> command must have
been previously used to define the lattice spacing. Each of these 3
quantities may be dependent on the x,y,z dimension, since the lattice
spacings can be different in x,y,z.</p>
</div>
<hr class="docutils" />
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info<a class="headerlink" href="#restart-fix-modify-output-run-start-stop-minimize-info" title="Permalink to this headline">¶</a></h2>
<p>This fix writes the original coordinates of moving atoms to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, as well as the initial timestep, so that
the motion can be continuous in a restarted simulation. See the
<a class="reference internal" href="read_restart.html"><em>read_restart</em></a> command for info on how to re-specify
a fix in an input script that reads a restart file, so that the
operation of the fix continues in an uninterrupted fashion.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Because the move positions are a function of the current
timestep and the initial timestep, you cannot reset the timestep to a
different value after reading a restart file, if you expect a fix move
command to work in an uninterrupted fashion.</p>
</div>
<p>None of the <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> options are relevant to this
fix.</p>
<p>This fix produces a per-atom array which can be accessed by various
<a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. The number of columns
for each atom is 3, and the columns store the original unwrapped x,y,z
coords of each atom. The per-atom values can be accessed on any
timestep.</p>
<p>No parameter of this fix can be used with the <em>start/stop</em> keywords of
the <a class="reference internal" href="run.html"><em>run</em></a> command. This fix is not invoked during <a class="reference internal" href="minimize.html"><em>energy minimization</em></a>.</p>
<p>For <a class="reference internal" href="run_style.html"><em>rRESPA time integration</em></a>, this fix adjusts the
position and velocity of atoms on the outermost rRESPA level.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
<blockquote>
<div>none</div></blockquote>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
<p><a class="reference internal" href="fix_nve.html"><em>fix nve</em></a>, <a class="reference internal" href="displace_atoms.html"><em>displace_atoms</em></a></p>
<p><strong>Default:</strong> none</p>
<p>The option default is units = lattice.</p>
</div>
</div>
</div>
</div>
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diff --git a/doc/fix_move.txt b/doc/fix_move.txt
index 88a291c6c..89bd37bf0 100644
--- a/doc/fix_move.txt
+++ b/doc/fix_move.txt
@@ -1,223 +1,226 @@
"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 move command :h3
[Syntax:]
fix ID group-ID move style args keyword values ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
move = style name of this fix command :l
style = {linear} or {wiggle} or {rotate} or {variable} :l
{linear} args = Vx Vy Vz
Vx,Vy,Vz = components of velocity vector (velocity units), any component can be specified as NULL
{wiggle} args = Ax Ay Az period
Ax,Ay,Az = components of amplitude vector (distance units), any component can be specified as NULL
period = period of oscillation (time units)
{rotate} args = Px Py Pz Rx Ry Rz period
Px,Py,Pz = origin point of axis of rotation (distance units)
Rx,Ry,Rz = axis of rotation vector
period = period of rotation (time units)
{variable} args = v_dx v_dy v_dz v_vx v_vy v_vz
v_dx,v_dy,v_dz = 3 variable names that calculate x,y,z displacement as function of time, any component can be specified as NULL
v_vx,v_vy,v_vz = 3 variable names that calculate x,y,z velocity as function of time, any component can be specified as NULL :pre
zero or more keyword/value pairs may be appended :l
keyword = {units} :l
{units} value = {box} or {lattice} :pre
:ule
[Examples:]
fix 1 boundary move wiggle 3.0 0.0 0.0 1.0 units box
fix 2 boundary move rotate 0.0 0.0 0.0 0.0 0.0 1.0 5.0
fix 2 boundary move variable v_myx v_myy NULL v_VX v_VY NULL :pre
[Description:]
Perform updates of position and velocity for atoms in the group each
timestep using the specified settings or formulas, without regard to
forces on the atoms. This can be useful for boundary or other atoms,
whose movement can influence nearby atoms.
NOTE: The atoms affected by this fix should not normally be time
integrated by other fixes (e.g. "fix nve"_fix_nve.html, "fix
nvt"_fix_nh.html), since that will change their positions and
velocities twice.
NOTE: As atoms move due to this fix, they will pass thru periodic
boundaries and be remapped to the other side of the simulation box,
just as they would during normal time integration (e.g. via the "fix
nve"_fix_nve.html command). It is up to you to decide whether
periodic boundaries are appropriate with the kind of atom motion you
are prescribing with this fix.
NOTE: As dicsussed below, atoms are moved relative to their initial
position at the time the fix is specified. These initial coordinates
are stored by the fix in "unwrapped" form, by using the image flags
associated with each atom. See the "dump custom"_dump.html command
for a discussion of "unwrapped" coordinates. See the Atoms section of
the "read_data"_read_data.html command for a discussion of image flags
and how they are set for each atom. You can reset the image flags
(e.g. to 0) before invoking this fix by using the "set image"_set.html
command.
:line
The {linear} style moves atoms at a constant velocity, so that their
position {X} = (x,y,z) as a function of time is given in vector
notation as
X(t) = X0 + V * delta :pre
where {X0} = (x0,y0,z0) is their position at the time the fix is
specified, {V} is the specified velocity vector with components
(Vx,Vy,Vz), and {delta} is the time elapsed since the fix was
specified. This style also sets the velocity of each atom to V =
(Vx,Vy,Vz). If any of the velocity components is specified as NULL,
then the position and velocity of that component is time integrated
the same as the "fix nve"_fix_nve.html command would perform, using
the corresponding force component on the atom.
Note that the {linear} style is identical to using the {variable}
style with an "equal-style variable"_variable.html that uses the
vdisplace() function. E.g.
variable V equal 10.0
variable x equal vdisplace(0.0,$V)
fix 1 boundary move variable v_x NULL NULL v_V NULL NULL :pre
The {wiggle} style moves atoms in an oscillatory fashion, so that
their position {X} = (x,y,z) as a function of time is given in vector
notation as
X(t) = X0 + A sin(omega*delta) :pre
where {X0} = (x0,y0,z0) is their position at the time the fix is
specified, {A} is the specified amplitude vector with components
(Ax,Ay,Az), {omega} is 2 PI / {period}, and {delta} is the time
elapsed since the fix was specified. This style also sets the
velocity of each atom to the time derivative of this expression. If
any of the amplitude components is specified as NULL, then the
position and velocity of that component is time integrated the same as
the "fix nve"_fix_nve.html command would perform, using the
corresponding force component on the atom.
Note that the {wiggle} style is identical to using the {variable}
style with "equal-style variables"_variable.html that use the
swiggle() and cwiggle() functions. E.g.
variable A equal 10.0
variable T equal 5.0
variable omega equal 2.0*PI/$T
variable x equal swiggle(0.0,$A,$T)
variable v equal v_omega*($A-cwiggle(0.0,$A,$T))
fix 1 boundary move variable v_x NULL NULL v_v NULL NULL :pre
The {rotate} style rotates atoms around a rotation axis {R} =
(Rx,Ry,Rz) that goes thru a point {P} = (Px,Py,Pz). The {period} of
-the rotation is also specified. This style also sets the velocity of
-each atom to (omega cross Rperp) where omega is its angular velocity
-around the rotation axis and Rperp is a perpendicular vector from the
-rotation axis to the atom. If the defined
-"atom_style"_atom_style.html assigns an angular velocity to each atom,
-then each atom's angular velocity is also set to omega. Note that the
-direction of rotation for the atoms around the rotation axis is
-consistent with the right-hand rule: if your right-hand's thumb points
-along {R}, then your fingers wrap around the axis in the direction of
-rotation.
+the rotation is also specified. The direction of rotation for the
+atoms around the rotation axis is consistent with the right-hand rule:
+if your right-hand thumb points along {R}, then your fingers wrap
+around the axis in the direction of rotation.
+
+This style also sets the velocity of each atom to (omega cross Rperp)
+where omega is its angular velocity around the rotation axis and Rperp
+is a perpendicular vector from the rotation axis to the atom. If the
+defined "atom_style"_atom_style.html assigns an angular velocity or
+angular moementum or orientation to each atom ("atom
+styles"_atom_style.html sphere, ellipsoid, line, tri, body), then
+those properties are also updated appropriately to correspond to the
+atom's motion and rotation over time.
The {variable} style allows the position and velocity components of
each atom to be set by formulas specified via the
"variable"_variable.html command. Each of the 6 variables is
specified as an argument to the fix as v_name, where name is the
variable name that is defined elsewhere in the input script.
Each variable must be of either the {equal} or {atom} style.
{Equal}-style variables compute a single numeric quantity, that can be
a function of the timestep as well as of other simulation values.
{Atom}-style variables compute a numeric quantity for each atom, that
can be a function per-atom quantities, such as the atom's position, as
well as of the timestep and other simulation values. Note that this
fix stores the original coordinates of each atom (see note below) so
that per-atom quantity can be used in an atom-style variable formula.
See the "variable"_variable.html command for details.
The first 3 variables (v_dx,v_dy,v_dz) specified for the {variable}
style are used to calculate a displacement from the atom's original
position at the time the fix was specified. The second 3 variables
(v_vx,v_vy,v_vz) specified are used to compute a velocity for each
atom.
Any of the 6 variables can be specified as NULL. If both the
displacement and velocity variables for a particular x,y,z component
are specified as NULL, then the position and velocity of that
component is time integrated the same as the "fix nve"_fix_nve.html
command would perform, using the corresponding force component on the
atom. If only the velocity variable for a component is specified as
NULL, then the displacement variable will be used to set the position
of the atom, and its velocity component will not be changed. If only
the displacement variable for a component is specified as NULL, then
the velocity variable will be used to set the velocity of the atom,
and the position of the atom will be time integrated using that
velocity.
The {units} keyword determines the meaning of the distance units used
to define the {linear} velocity and {wiggle} amplitude and {rotate}
origin. This setting is ignored for the {variable} style. A {box}
value selects standard units as defined by the "units"_units.html
command, e.g. velocity in Angstroms/fmsec and amplitude and position
in Angstroms for units = real. A {lattice} value means the velocity
units are in lattice spacings per time and the amplitude and position
are in lattice spacings. The "lattice"_lattice.html command must have
been previously used to define the lattice spacing. Each of these 3
quantities may be dependent on the x,y,z dimension, since the lattice
spacings can be different in x,y,z.
:line
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix writes the original coordinates of moving atoms to "binary
restart files"_restart.html, as well as the initial timestep, so that
the motion can be continuous in a restarted simulation. See the
"read_restart"_read_restart.html command for info on how to re-specify
a fix in an input script that reads a restart file, so that the
operation of the fix continues in an uninterrupted fashion.
NOTE: Because the move positions are a function of the current
timestep and the initial timestep, you cannot reset the timestep to a
different value after reading a restart file, if you expect a fix move
command to work in an uninterrupted fashion.
None of the "fix_modify"_fix_modify.html options are relevant to this
fix.
This fix produces a per-atom array which can be accessed by various
"output commands"_Section_howto.html#howto_15. The number of columns
for each atom is 3, and the columns store the original unwrapped x,y,z
coords of each atom. The per-atom values can be accessed on any
timestep.
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
For "rRESPA time integration"_run_style.html, this fix adjusts the
position and velocity of atoms on the outermost rRESPA level.
[Restrictions:] none
[Related commands:]
"fix nve"_fix_nve.html, "displace_atoms"_displace_atoms.html
[Default:] none
The option default is units = lattice.
diff --git a/doc/fix_store_state.html b/doc/fix_store_state.html
index 34de29af8..e96eb5e76 100644
--- a/doc/fix_store_state.html
+++ b/doc/fix_store_state.html
@@ -1,316 +1,316 @@
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<div class="section" id="fix-store-state-command">
<span id="index-0"></span><h1>fix store/state command<a class="headerlink" href="#fix-store-state-command" title="Permalink to this headline">¶</a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
<div class="highlight-python"><div class="highlight"><pre>fix ID group-ID store/state N input1 input2 ... keyword value ...
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><em>fix</em></a> command</li>
<li>store/state = style name of this fix command</li>
<li>N = store atom attributes every N steps, N = 0 for initial store only</li>
<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, xsu, ysu, zsu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
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></div>
</div>
<div class="highlight-python"><div class="highlight"><pre>id = atom ID
mol = molecule ID
type = atom type
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
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
c_ID = per-atom vector calculated by a compute with ID
c_ID[I] = Ith column of per-atom array calculated by a compute with ID
f_ID = per-atom vector calculated by a fix with ID
f_ID[I] = Ith column of per-atom array calculated by a fix with ID
v_name = per-atom vector calculated by an atom-style variable with name
d_name = per-atom floating point vector name, managed by fix property/atom
i_name = per-atom integer vector name, managed by fix property/atom
</pre></div>
</div>
<ul class="simple">
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>com</em></li>
</ul>
<pre class="literal-block">
<em>com</em> value = <em>yes</em> or <em>no</em>
</pre>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
<div class="highlight-python"><div class="highlight"><pre>fix 1 all store/state 0 x y z
fix 1 all store/state 0 xu yu zu com yes
fix 2 all store/state 1000 vx vy vz
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>Define a fix that stores attributes for each atom in the group at the
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.</p>
<p>If <em>N</em> is not zero, then the attributes will be updated every <em>N</em>
steps.</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 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> 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.</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>
</div>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info<a class="headerlink" href="#restart-fix-modify-output-run-start-stop-minimize-info" title="Permalink to this headline">¶</a></h2>
<p>This fix writes the per-atom values it stores to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so that the values can be restored when a
simulation is restarted. See the <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
uninterrupted fashion.</p>
<p>None of the <a class="reference internal" href="fix_modify.html"><em>fix_modify</em></a> options are relevant to this
fix.</p>
<p>If a single input is specified, this fix produces a per-atom vector.
If multiple inputs are specified, a per-atom array is produced where
the number of columns for each atom is the number of inputs. These
can be accessed by various <a class="reference internal" href="Section_howto.html#howto-15"><span>output commands</span></a>. The per-atom values be
accessed on any timestep.</p>
<p>No parameter of this fix can be used with the <em>start/stop</em> keywords of
the <a class="reference internal" href="run.html"><em>run</em></a> command. This fix is not invoked during <a class="reference internal" href="minimize.html"><em>energy minimization</em></a>.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
<blockquote>
<div>none</div></blockquote>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
<p><a class="reference internal" href="dump.html"><em>dump custom</em></a>, <a class="reference internal" href="compute_property_atom.html"><em>compute property/atom</em></a>,
<a class="reference internal" href="fix_property_atom.html"><em>fix property/atom</em></a>, <a class="reference internal" href="variable.html"><em>variable</em></a></p>
</div>
<div class="section" id="default">
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
<p>The option default is com = no.</p>
</div>
</div>
</div>
</div>
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diff --git a/doc/fix_store_state.txt b/doc/fix_store_state.txt
index 2afabdc52..6521f078b 100644
--- a/doc/fix_store_state.txt
+++ b/doc/fix_store_state.txt
@@ -1,129 +1,129 @@
"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 store/state command :h3
[Syntax:]
fix ID group-ID store/state N input1 input2 ... keyword value ... :pre
ID, group-ID are documented in "fix"_fix.html command :ulb,l
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, xsu, ysu, zsu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
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
id = atom ID
mol = molecule ID
type = atom type
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
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
c_ID = per-atom vector calculated by a compute with ID
c_ID\[I\] = Ith column of per-atom array calculated by a compute with ID
f_ID = per-atom vector calculated by a fix with ID
f_ID\[I\] = Ith column of per-atom array calculated by a fix with ID
v_name = per-atom vector calculated by an atom-style variable with name
d_name = per-atom floating point vector name, managed by fix property/atom
i_name = per-atom integer vector name, managed by fix property/atom :pre
zero or more keyword/value pairs may be appended :l
keyword = {com} :l
{com} value = {yes} or {no} :pre
:ule
[Examples:]
fix 1 all store/state 0 x y z
fix 1 all store/state 0 xu yu zu com yes
fix 2 all store/state 1000 vx vy vz :pre
[Description:]
Define a fix that stores attributes for each atom in the group at the
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.
If {N} is not zero, then the attributes will be updated every {N}
steps.
-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.
+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.
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.
[Restart, fix_modify, output, run start/stop, minimize info:]
This fix writes the per-atom values it stores to "binary restart
files"_restart.html, so that the values can be restored when a
simulation is restarted. See the "read_restart"_read_restart.html
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
uninterrupted fashion.
None of the "fix_modify"_fix_modify.html options are relevant to this
fix.
If a single input is specified, this fix produces a per-atom vector.
If multiple inputs are specified, a per-atom array is produced where
the number of columns for each atom is the number of inputs. These
can be accessed by various "output
commands"_Section_howto.html#howto_15. The per-atom values be
accessed on any timestep.
No parameter of this fix can be used with the {start/stop} keywords of
the "run"_run.html command. This fix is not invoked during "energy
minimization"_minimize.html.
[Restrictions:] none
[Related commands:]
"dump custom"_dump.html, "compute
property/atom"_compute_property_atom.html,
"fix property/atom"_fix_property_atom.html, "variable"_variable.html
[Default:]
The option default is com = no.
diff --git a/doc/pair_beck.html b/doc/pair_beck.html
index f58e89837..81cf482da 100644
--- a/doc/pair_beck.html
+++ b/doc/pair_beck.html
@@ -1,282 +1,282 @@
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<div class="section" id="pair-style-beck-command">
<span id="index-0"></span><h1>pair_style beck command<a class="headerlink" href="#pair-style-beck-command" title="Permalink to this headline">¶</a></h1>
</div>
<div class="section" id="pair-style-beck-gpu-command">
<h1>pair_style beck/gpu command<a class="headerlink" href="#pair-style-beck-gpu-command" title="Permalink to this headline">¶</a></h1>
</div>
<div class="section" id="pair-style-beck-omp-command">
<h1>pair_style beck/omp command<a class="headerlink" href="#pair-style-beck-omp-command" title="Permalink to this headline">¶</a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
<div class="highlight-python"><div class="highlight"><pre>pair_style beck Rc
</pre></div>
</div>
<ul class="simple">
<li>Rc = cutoff for interactions (distance units)</li>
</ul>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
<div class="highlight-python"><div class="highlight"><pre>pair_style beck 8.0
pair_coeff * * 399.671876712 0.0000867636112694 0.675 4.390 0.0003746
pair_coeff 1 1 399.671876712 0.0000867636112694 0.675 4.390 0.0003746 6.0
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>Style <em>beck</em> computes interactions based on the potential by
<a class="reference internal" href="#beck"><span>(Beck)</span></a>, originally designed for simulation of Helium. It
includes truncation at a cutoff distance Rc.</p>
<img alt="_images/pair_beck.jpg" class="align-center" src="_images/pair_beck.jpg" />
<p>The following coefficients must be defined for each pair of atoms
types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command as in the examples
above, or in the data file or restart files read by the
<a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands.</p>
<ul class="simple">
<li>A (energy units)</li>
<li>B (energy-distance^6 units)</li>
<li>a (distance units)</li>
<li>alpha (1/distance units)</li>
<li>beta (1/distance^6 units)</li>
<li>cutoff (distance units)</li>
</ul>
<p>The last coefficient is optional. If not specified, the global cutoff
Rc is used.</p>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
<p>For atom type pairs I,J and I != J, coeffiecients must be specified.
-No default miture rules are used.</p>
+No default mixing rules are used.</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> shift
option for the energy of the pair interaction.</p>
<p>The <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a> table option is not relevant
for this pair style.</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
tail option for adding long-range tail corrections.</p>
<p>This pair style writes its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.</p>
<p>This pair style can only be used via the <em>pair</em> keyword of the
<a class="reference internal" href="run_style.html"><em>run_style respa</em></a> command. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
<blockquote>
<div>none</div></blockquote>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
<p><a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a></p>
<p><strong>Default:</strong> none</p>
<hr class="docutils" />
<p id="beck"><strong>(Beck)</strong> Beck, Molecular Physics, 14, 311 (1968).</p>
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diff --git a/doc/pair_beck.txt b/doc/pair_beck.txt
index b3ae94bdf..1b2309ef7 100644
--- a/doc/pair_beck.txt
+++ b/doc/pair_beck.txt
@@ -1,109 +1,109 @@
"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
pair_style beck command :h3
pair_style beck/gpu command :h3
pair_style beck/omp command :h3
[Syntax:]
pair_style beck Rc :pre
Rc = cutoff for interactions (distance units) :ul
[Examples:]
pair_style beck 8.0
pair_coeff * * 399.671876712 0.0000867636112694 0.675 4.390 0.0003746
pair_coeff 1 1 399.671876712 0.0000867636112694 0.675 4.390 0.0003746 6.0 :pre
[Description:]
Style {beck} computes interactions based on the potential by
"(Beck)"_#Beck, originally designed for simulation of Helium. It
includes truncation at a cutoff distance Rc.
:c,image(Eqs/pair_beck.jpg)
The following coefficients must be defined for each pair of atoms
types via the "pair_coeff"_pair_coeff.html command as in the examples
above, or in the data file or restart files read by the
"read_data"_read_data.html or "read_restart"_read_restart.html
commands.
A (energy units)
B (energy-distance^6 units)
a (distance units)
alpha (1/distance units)
beta (1/distance^6 units)
cutoff (distance units) :ul
The last coefficient is optional. If not specified, the global cutoff
Rc is used.
:line
Styles with a {cuda}, {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in "Section_accelerate"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section_accelerate"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
For atom type pairs I,J and I != J, coeffiecients must be specified.
-No default miture rules are used.
+No default mixing rules are used.
This pair style does not support the "pair_modify"_pair_modify.html shift
option for the energy of the pair interaction.
The "pair_modify"_pair_modify.html table option is not relevant
for this pair style.
This pair style does not support the "pair_modify"_pair_modify.html
tail option for adding long-range tail corrections.
This pair style writes its information to "binary restart
files"_restart.html, so pair_style and pair_coeff commands do not need
to be specified in an input script that reads a restart file.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords.
:line
[Restrictions:] none
[Related commands:]
"pair_coeff"_pair_coeff.html
[Default:] none
:line
:link(Beck)
[(Beck)] Beck, Molecular Physics, 14, 311 (1968).
diff --git a/doc/pair_line_lj.html b/doc/pair_line_lj.html
index 114a88a87..62c96afb9 100644
--- a/doc/pair_line_lj.html
+++ b/doc/pair_line_lj.html
@@ -1,302 +1,334 @@
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<div class="section" id="pair-style-line-lj-command">
<span id="index-0"></span><h1>pair_style line/lj command<a class="headerlink" href="#pair-style-line-lj-command" title="Permalink to this headline">¶</a></h1>
</div>
<div class="section" id="pair-style-line-lj-omp-command">
<h1>pair_style line/lj/omp command<a class="headerlink" href="#pair-style-line-lj-omp-command" title="Permalink to this headline">¶</a></h1>
<div class="section" id="syntax">
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
<div class="highlight-python"><div class="highlight"><pre>pair_style line/lj cutoff
</pre></div>
</div>
<p>cutoff = global cutoff for interactions (distance units)</p>
</div>
<div class="section" id="examples">
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
<div class="highlight-python"><div class="highlight"><pre>pair_style line/lj 3.0
-pair_coeff * * 1.0 1.0
-pair_coeff 1 1 1.0 1.5 2.5
+pair_coeff * * 1.0 1.0 1.0 0.8 1.12
+pair_coeff 1 2 1.0 2.0 1.0 1.5 1.12 5.0
+pair_coeff 1 2 1.0 0.0 1.0 1.0 2.5
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
<p>Style <em>line/lj</em> treats particles which are line segments as a set of
small spherical particles that tile the line segment length as
explained below. Interactions between two line segments, each with N1
and N2 spherical particles, are calculated as the pairwise sum of
N1*N2 Lennard-Jones interactions. Interactions between a line segment
with N spherical particles and a point particle are treated as the
pairwise sum of N Lennard-Jones interactions. See the <a class="reference internal" href="pair_lj.html"><em>pair_style lj/cut</em></a> doc page for the definition of Lennard-Jones
interactions.</p>
-<p>The cutoff distance for an interaction between 2 line segments, or
-between a line segment and a point particle, is calculated from the
-position of the line segment (its center), not between pairs of
-individual spheres comprising the line segment. Thus an interaction
-is either calculated in its entirety or not at all.</p>
-<p>The set of non-overlapping spherical particles that represent a line
-segment, for purposes of this pair style, are generated in the
-following manner. Their size is a function of the line segment length
-and the specified sigma for that particle type. If a line segment has
-a length L and is of type I, then the number of spheres N that
-represent the segment is calculated as N = L/sigma_II, rounded up to
-an integer value. Thus if L is not evenly divisibly by sigam_II, N is
-incremented to include one extra sphere. In this case, the spheres
-must be slightly smaller than sigma_II so as not to overlap, so a new
-sigma-prime is chosen as the sphere diameter, such that L/N =
-sigma-prime. Thus the line segment interacts with other segments or
-point particles as a collection of N spheres of diameter sigma-prime,
-evenly spaced along the line segment, so as to exactly cover its
-length.</p>
-<p>The LJ interaction between 2 spheres on different line segments of
-types I,J is computed with an arithmetic mixing of the sigma values of
-the 2 spheres and using the specified epsilon value for I,J atom
-types. Note that because the sigma values for line segment spheres is
-computed using only sigma_II values, specific to the line segment’s
-type, this means that any specified sigma_IJ values (for I != J) are
-effectively ignored.</p>
+<p>The set of non-overlapping spherical sub-particles that represent a
+line segment are generated in the following manner. Their size is a
+function of the line segment length and the specified sub-particle
+size for that particle type. If a line segment has a length L and is
+of type I, then the number of spheres N that represent the segment is
+calculated as N = L/sizeI, rounded up to an integer value. Thus if L
+is not evenly divisibly by sizeI, N is incremented to include one
+extra sphere. The centers of the spheres are spaced equally along the
+line segment. Imagine N+1 equally-space points, which include the 2
+end points of the segment. The sphere centers are halfway between
+each pair of points.</p>
+<p>The LJ interaction between 2 spheres on different line segments (or a
+sphere on a line segment and a point particles) is computed with
+sub-particle epsilon, sigma, and cutoff values that are set by the
+pair_coeff command, as described below. If the distance bewteen the 2
+spheres is greater than the sub-particle cutoff, there is no
+interaction. This means that some pairs of sub-particles on 2 line
+segments may interact, but others may not.</p>
+<p>For purposes of creating the neighbor list for pairs of interacting
+line segments or lines/point particles, a regular particle-particle
+cutoff is used, as defined by the <em>cutoff</em> setting above in the
+pair_style command or overridden with an optional argument in the
+pair_coeff command for a type pair as discussed below. The distance
+between the centers of 2 line segments, or the center of a line
+segment and a point particle, must be less than this distance (plus
+the neighbor skin; see the <a class="reference external" href="neighbor">neighbor</a> command), for the pair
+of particles to be included in the neighbor list.</p>
+<div class="admonition note">
+<p class="first admonition-title">Note</p>
+<p class="last">This means that a too-short value for the <em>cutoff</em> setting can
+exclude a pair of particles from the neighbor list even if pairs of
+their sub-particle spheres would interact, based on the sub-particle
+cutoff specified in the pair_coeff command. E.g. sub-particles at the
+ends of the line segments that are close to each other. Which may not
+be what you want, since it means the ends of 2 line segments could
+pass through each other. It is up to you to specify a <em>cutoff</em>
+setting that is consistent with the length of the line segments you
+are using and the sub-particle cutoff settings.</p>
+</div>
<p>For style <em>line/lj</em>, the following coefficients must be defined for
-each pair of atoms types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command
+each pair of atom types via the <a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a> command
as in the examples above, or in the data file or restart files read by
the <a class="reference internal" href="read_data.html"><em>read_data</em></a> or <a class="reference internal" href="read_restart.html"><em>read_restart</em></a>
commands:</p>
<ul class="simple">
+<li>sizeI (distance units)</li>
+<li>sizeJ (distance units)</li>
<li>epsilon (energy units)</li>
<li>sigma (distance units)</li>
+<li>subcutoff (distance units)</li>
<li>cutoff (distance units)</li>
</ul>
-<p>The last coefficient is optional. If not specified, the global cutoff
-is used.</p>
+<p>The <em>sizeI</em> and <em>sizeJ</em> coefficients are the sub-particle sizes for
+line particles of type I and type J. They are used to define the N
+sub-particles per segment as described above. These coefficients are
+actually stored on a per-type basis. Thus if there are multiple
+pair_coeff commmands that involve type I, as either the first or
+second atom type, you should use consistent values for sizeI or sizeJ
+in all of them. If you do not do this, the last value specified for
+sizeI will apply to all segments of type I. If typeI or typeJ refers
+to point particles, the corresponding sizeI or sizeJ is ignored; it
+can be set to 0.0.</p>
+<p>The <em>epsilon</em>, <em>sigma</em>, and <em>subcutoff</em> coefficients are used to
+compute an LJ interactions between a pair of sub-particles on 2 line
+segments (of type I and J), or between a sub particle/point particle
+pair. As discussed above, the <em>subcutoff</em> and <em>cutoff</em> params are
+different. The latter is only used for building the neighbor list
+when the distance between centers of two line segments or one segment
+and a point particle is calculated.</p>
+<p>The <em>cutoff</em> coefficient is optional. If not specified, the global
+cutoff is used.</p>
<hr class="docutils" />
<p>Styles with a <em>cuda</em>, <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a>
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.</p>
<p>These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the <a class="reference internal" href="Section_start.html#start-3"><span>Making LAMMPS</span></a> section for more info.</p>
<p>You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the <a class="reference internal" href="Section_start.html#start-7"><span>-suffix command-line switch</span></a> when you invoke LAMMPS, or you can
use the <a class="reference internal" href="suffix.html"><em>suffix</em></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><em>Section_accelerate</em></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
<hr class="docutils" />
<p><strong>Mixing, shift, table, tail correction, restart, rRESPA info</strong>:</p>
-<p>For atom type pairs I,J and I != J, the epsilon and sigma coefficients
-and cutoff distance for all of this pair style can be mixed. The
-default mix value is <em>geometric</em>. See the “pair_modify” command for
-details.</p>
+<p>For atom type pairs I,J and I != J, coeffiecients must be specified.
+No default mixing rules are used.</p>
<p>This pair style does not support the <a class="reference internal" href="pair_modify.html"><em>pair_modify</em></a>
shift, table, and tail options.</p>
<p>This pair style does not write its information to <a class="reference internal" href="restart.html"><em>binary restart files</em></a>.</p>
<p>This pair style can only be used via the <em>pair</em> keyword of the
<a class="reference internal" href="run_style.html"><em>run_style respa</em></a> command. It does not support the
<em>inner</em>, <em>middle</em>, <em>outer</em> keywords.</p>
</div>
<hr class="docutils" />
<div class="section" id="restrictions">
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
<p>This style is part of the ASPHERE package. It is only enabled if
LAMMPS was built with that package. See the <span class="xref std std-ref">Making LAMMPS</span> section for more info.</p>
<p>Defining particles to be line segments so they participate in
line/line or line/particle interactions requires the use the
<a class="reference internal" href="atom_style.html"><em>atom_style line</em></a> command.</p>
</div>
<div class="section" id="related-commands">
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
<p><a class="reference internal" href="pair_coeff.html"><em>pair_coeff</em></a>, <a class="reference internal" href="pair_tri_lj.html"><em>pair_style tri/lj</em></a></p>
<p><strong>Default:</strong> none</p>
</div>
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\ No newline at end of file
diff --git a/doc/pair_line_lj.txt b/doc/pair_line_lj.txt
index c467a9876..5ba08d4f3 100644
--- a/doc/pair_line_lj.txt
+++ b/doc/pair_line_lj.txt
@@ -1,136 +1,168 @@
"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
pair_style line/lj command :h3
pair_style line/lj/omp command :h3
[Syntax:]
pair_style line/lj cutoff :pre
cutoff = global cutoff for interactions (distance units)
[Examples:]
pair_style line/lj 3.0
-pair_coeff * * 1.0 1.0
-pair_coeff 1 1 1.0 1.5 2.5 :pre
+pair_coeff * * 1.0 1.0 1.0 0.8 1.12
+pair_coeff 1 2 1.0 2.0 1.0 1.5 1.12 5.0
+pair_coeff 1 2 1.0 0.0 1.0 1.0 2.5 :pre
[Description:]
Style {line/lj} treats particles which are line segments as a set of
small spherical particles that tile the line segment length as
explained below. Interactions between two line segments, each with N1
and N2 spherical particles, are calculated as the pairwise sum of
N1*N2 Lennard-Jones interactions. Interactions between a line segment
with N spherical particles and a point particle are treated as the
pairwise sum of N Lennard-Jones interactions. See the "pair_style
lj/cut"_pair_lj.html doc page for the definition of Lennard-Jones
interactions.
-The cutoff distance for an interaction between 2 line segments, or
-between a line segment and a point particle, is calculated from the
-position of the line segment (its center), not between pairs of
-individual spheres comprising the line segment. Thus an interaction
-is either calculated in its entirety or not at all.
-
-The set of non-overlapping spherical particles that represent a line
-segment, for purposes of this pair style, are generated in the
-following manner. Their size is a function of the line segment length
-and the specified sigma for that particle type. If a line segment has
-a length L and is of type I, then the number of spheres N that
-represent the segment is calculated as N = L/sigma_II, rounded up to
-an integer value. Thus if L is not evenly divisibly by sigam_II, N is
-incremented to include one extra sphere. In this case, the spheres
-must be slightly smaller than sigma_II so as not to overlap, so a new
-sigma-prime is chosen as the sphere diameter, such that L/N =
-sigma-prime. Thus the line segment interacts with other segments or
-point particles as a collection of N spheres of diameter sigma-prime,
-evenly spaced along the line segment, so as to exactly cover its
-length.
-
-The LJ interaction between 2 spheres on different line segments of
-types I,J is computed with an arithmetic mixing of the sigma values of
-the 2 spheres and using the specified epsilon value for I,J atom
-types. Note that because the sigma values for line segment spheres is
-computed using only sigma_II values, specific to the line segment's
-type, this means that any specified sigma_IJ values (for I != J) are
-effectively ignored.
+The set of non-overlapping spherical sub-particles that represent a
+line segment are generated in the following manner. Their size is a
+function of the line segment length and the specified sub-particle
+size for that particle type. If a line segment has a length L and is
+of type I, then the number of spheres N that represent the segment is
+calculated as N = L/sizeI, rounded up to an integer value. Thus if L
+is not evenly divisibly by sizeI, N is incremented to include one
+extra sphere. The centers of the spheres are spaced equally along the
+line segment. Imagine N+1 equally-space points, which include the 2
+end points of the segment. The sphere centers are halfway between
+each pair of points.
+
+The LJ interaction between 2 spheres on different line segments (or a
+sphere on a line segment and a point particles) is computed with
+sub-particle epsilon, sigma, and cutoff values that are set by the
+pair_coeff command, as described below. If the distance bewteen the 2
+spheres is greater than the sub-particle cutoff, there is no
+interaction. This means that some pairs of sub-particles on 2 line
+segments may interact, but others may not.
+
+For purposes of creating the neighbor list for pairs of interacting
+line segments or lines/point particles, a regular particle-particle
+cutoff is used, as defined by the {cutoff} setting above in the
+pair_style command or overridden with an optional argument in the
+pair_coeff command for a type pair as discussed below. The distance
+between the centers of 2 line segments, or the center of a line
+segment and a point particle, must be less than this distance (plus
+the neighbor skin; see the "neighbor"_neighbor command), for the pair
+of particles to be included in the neighbor list.
+
+NOTE: This means that a too-short value for the {cutoff} setting can
+exclude a pair of particles from the neighbor list even if pairs of
+their sub-particle spheres would interact, based on the sub-particle
+cutoff specified in the pair_coeff command. E.g. sub-particles at the
+ends of the line segments that are close to each other. Which may not
+be what you want, since it means the ends of 2 line segments could
+pass through each other. It is up to you to specify a {cutoff}
+setting that is consistent with the length of the line segments you
+are using and the sub-particle cutoff settings.
For style {line/lj}, the following coefficients must be defined for
-each pair of atoms types via the "pair_coeff"_pair_coeff.html command
+each pair of atom types via the "pair_coeff"_pair_coeff.html command
as in the examples above, or in the data file or restart files read by
the "read_data"_read_data.html or "read_restart"_read_restart.html
commands:
+sizeI (distance units)
+sizeJ (distance units)
epsilon (energy units)
sigma (distance units)
+subcutoff (distance units)
cutoff (distance units) :ul
-The last coefficient is optional. If not specified, the global cutoff
-is used.
+The {sizeI} and {sizeJ} coefficients are the sub-particle sizes for
+line particles of type I and type J. They are used to define the N
+sub-particles per segment as described above. These coefficients are
+actually stored on a per-type basis. Thus if there are multiple
+pair_coeff commmands that involve type I, as either the first or
+second atom type, you should use consistent values for sizeI or sizeJ
+in all of them. If you do not do this, the last value specified for
+sizeI will apply to all segments of type I. If typeI or typeJ refers
+to point particles, the corresponding sizeI or sizeJ is ignored; it
+can be set to 0.0.
+
+The {epsilon}, {sigma}, and {subcutoff} coefficients are used to
+compute an LJ interactions between a pair of sub-particles on 2 line
+segments (of type I and J), or between a sub particle/point particle
+pair. As discussed above, the {subcutoff} and {cutoff} params are
+different. The latter is only used for building the neighbor list
+when the distance between centers of two line segments or one segment
+and a point particle is calculated.
+
+The {cutoff} coefficient is optional. If not specified, the global
+cutoff is used.
:line
Styles with a {cuda}, {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
functionally the same as the corresponding style without the suffix.
They have been optimized to run faster, depending on your available
hardware, as discussed in "Section_accelerate"_Section_accelerate.html
of the manual. The accelerated styles take the same arguments and
should produce the same results, except for round-off and precision
issues.
These accelerated styles are part of the USER-CUDA, GPU, USER-INTEL,
KOKKOS, USER-OMP and OPT packages, respectively. They are only
enabled if LAMMPS was built with those packages. See the "Making
LAMMPS"_Section_start.html#start_3 section for more info.
You can specify the accelerated styles explicitly in your input script
by including their suffix, or you can use the "-suffix command-line
switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can
use the "suffix"_suffix.html command in your input script.
See "Section_accelerate"_Section_accelerate.html of the manual for
more instructions on how to use the accelerated styles effectively.
:line
[Mixing, shift, table, tail correction, restart, rRESPA info]:
-For atom type pairs I,J and I != J, the epsilon and sigma coefficients
-and cutoff distance for all of this pair style can be mixed. The
-default mix value is {geometric}. See the "pair_modify" command for
-details.
+For atom type pairs I,J and I != J, coeffiecients must be specified.
+No default mixing rules are used.
This pair style does not support the "pair_modify"_pair_modify.html
shift, table, and tail options.
This pair style does not write its information to "binary restart
files"_restart.html.
This pair style can only be used via the {pair} keyword of the
"run_style respa"_run_style.html command. It does not support the
{inner}, {middle}, {outer} keywords.
:line
[Restrictions:]
This style is part of the ASPHERE package. It is only enabled if
LAMMPS was built with that package. See the "Making
LAMMPS"_Section_start.html#2_3 section for more info.
Defining particles to be line segments so they participate in
line/line or line/particle interactions requires the use the
"atom_style line"_atom_style.html command.
[Related commands:]
"pair_coeff"_pair_coeff.html, "pair_style tri/lj"_pair_tri_lj.html
[Default:] none
diff --git a/doc/searchindex.js b/doc/searchindex.js
index 3f867802f..f810e90bb 100644
--- a/doc/searchindex.js
+++ b/doc/searchindex.js
@@ -1 +1 @@
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li:431,child:8,chip:[7,12,17,18,370,482],chipot:219,chiral:349,chmod:[11,12],cho:419,chocol:[7,194],choic:[3,6,12,15,16,18,40,41,54,87,143,146,147,161,172,188,206,210,211,214,217,220,221,233,239,242,253,255,282,290,299,321,350,356,361,362,365,367,370,402,415,424,428,469,478,479,482,483,489,490,494],choos:[1,3,6,7,8,12,16,17,18,29,39,54,87,119,158,159,193,215,216,217,218,221,228,239,242,253,255,257,258,259,260,261,262,263,286,314,318,332,355,356,362,459,464,466,478,484],chose:[453,455],chosen:[2,3,6,12,17,142,168,171,180,188,193,199,204,218,221,228,231,232,240,242,253,255,260,282,285,296,314,318,321,322,327,329,330,336,356,357,362,370,395,399,405,406,409,435,453,464,478,483,490],chri:166,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[66,75,90,94,105,107,116,148,163,165,206],chute:[4,10,234],ciccotti:302,cieplak:[6,174,481],cii:207,cij:207,circl:[42,71,310],circular:[3,6,146,189],circumst:18,circumv:[92,108,294],citat:[],cite:[3,7,8,12,239,440],ckio:2,cko:2,cl1:167,clarendon:[29,390],clarifi:[7,453,455],clariti:339,clark:427,class2:[],classic:[0,3,5,6,7,8,9,229,282,289,294,326,351,395],classifi:[9,450,458],claus:467,clean:[6,12,14,15,17,477],cleanli:[468,498],clear:[],clearli:7,clebsch:142,clermont:[9,13],clever:473,click:[2,11,22,37,44,55,168,176,187,193,236,341,350,365,384,450],client:[236,238],climb:[254,365,483],clinic:[7,13],clo:[157,190,496],clock:[12,464,483],clockwis:332,close:[3,6,11,12,13,39,41,67,71,143,171,191,216,217,218,233,240,242,255,276,299,302,332,335,354,356,359,361,362,365,370,372,377,387,388,419,424,436,438,455,473,479,490,492],closer:[3,41,118,166,190,191,214,218,222,323,365],closest:[216,280,299,329,398,434,449,459],cloud:[440,490],clovertown:18,clsuter:72,clump1:[284,299],clump2:[284,299],clump3:[284,299],clump:299,cluster:[],clutter:[3,9],cmap:469,cmatrix:233,cmax:419,cmd:[11,12,282,480],cmdarg:11,cmin:419,cmm:[],cn1:207,cn2:207,cna:[],cnn:207,cnr:[9,13],cnt:[402,473],co2:[40,167,302,364],coars:[7,9,29,36,40,54,180,284,299,314,400,435,481],coarser:[356,495],coarsest:142,code:[],coeff:[3,7,8,12,21,22,33,44,50,174,175,176,181,340,341,347,384,402,406,424,437,439,442,469],coeffcient:469,coeffici:[],coefficienct:391,coefficient0:393,coefficient1:393,coeffieci:[6,374],coeffincientn:393,coexist:[9,231,395],cohes:[6,396,419],coincid:[124,335,382,416,417,464],colberg:192,cold:[6,153,231,235,366,490],coldest:322,coleman8:9,coleman:[9,120,167,300],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,83,90,94,99,105,107,116,148,156,163,165,168,191,194,206,219,245,251,284,294,297,299,337,355,364,366,385,405,469,476,482,488,499],collid:[225,314,336],colliex:167,collinear:[3,284],collis:[3,242,314,332,336,392,399,462],colllis:314,colloid:[],colombo:39,colon:[195,337,470],color1:194,color2:194,color:[3,9,41,191,193,194,214,232,289,294],column:[3,6,9,12,13,42,63,65,66,67,68,69,71,75,77,79,81,90,92,93,94,105,107,108,110,112,115,116,117,118,119,121,142,143,148,156,163,165,166,167,188,191,194,197,205,206,207,209,210,211,212,245,252,253,289,299,315,316,326,336,397,401,432,433,470,484,486,495],colvar:[],colvarmodul:12,com:[],comamnd:220,comand:217,comannd:370,comb3:[],comb:[],comb_1:291,comb_2:291,combiant:388,combin:[3,6,7,9,11,13,36,40,63,65,69,79,87,93,104,110,117,146,147,161,191,193,203,209,236,245,255,282,288,318,327,335,338,340,355,356,358,362,370,385,387,388,395,396,402,414,415,441,451,453,455,458,461,472,477,482,490,495],come:[],comfort:[12,13],comm:[0,3,11,12,61,73,192,236,238,239,356,365,370,391,424,429,452,471],comm_modifi:[],comm_modift:61,comm_styl:[],comm_world:11,command:[],comment:[2,7,11,12,38,56,174,188,191,240,299,326,364,365,371,393,394,396,406,419,426,433,440,441,451,452,453,454,455,458,466,467,469,490,495],commerci:7,commmand:[3,6,12,59,109,277,463,464,466,483,498],common:[],commonli:[3,6,12,17,25,57,59,106,108,170,191,193,195,351,400,409,441,453,455,469,472,481],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,171,172,193,194,214,215,216,218,219,220,236,238,242,244,245,246,255,281,288,290,291,292,299,314,326,337,353,355,366,367,368,370,392,428,466,467,478,479,495,497,499],communc:355,comp:[7,192,238,239,302,356,365,395,424,429,434,448,452,454],compact:[63,197,384,450],compani:[5,7],compar:[1,3,4,6,8,12,17,39,86,112,120,151,166,167,176,187,194,224,290,337,339,355,356,363,365,419,440,464,483,484,490,494],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,175,176,187,340,341,350,383,450],compat:[3,5,7,8,9,11,12,13,17,18,41,71,119,121,179,191,195,199,205,206,207,209,210,211,212,214,281,293,318,321,328,331,334,355,370,403,422,424,452,466,467,495],compens:[6,215,216,297,366,395],compet:325,competit:356,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,166,191,192,193,195,236,325,356,370,422,469,470,474,495],compl:17,complain:[12,17],complement:419,complementari:[7,387,407],complet:[3,6,9,11,12,15,41,59,71,194,210,214,219,245,282,285,288,314,325,327,339,354,365,370,396,437,439,457,464,469,474,477,481,483,486,490,495],complex:[6,8,11,12,13,25,40,42,62,92,108,142,144,156,168,169,242,310,335,353,365,395,422,452,467,469,472,495],compli:[321,325],complic:[6,7,9,12,13,204,231,467],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,88,89,90,91,92,94,95,98,105,106,107,108,109,110,111,112,114,115,119,129,132,133,134,135,138,139,140,142,143,145,146,147,148,149,150,151,152,153,154,155,156,157,158,160,161,163,164,165,190,191,193,194,200,201,205,206,207,208,209,210,211,212,213,217,218,220,221,226,229,234,238,239,242,245,247,251,252,254,255,256,260,261,262,263,274,275,276,278,279,281,282,283,286,297,299,301,302,303,307,308,311,314,317,318,319,321,328,329,334,335,336,355,358,362,363,364,365,370,376,391,395,399,416,417,437,439,440,441,469,470,479,487,495,496],componenet:6,composit:[6,204,242,393],compound:[386,395,396,458],compres:[71,116,206],compress:[],compris:[40,335,405,434,457],compton:[120,167],comptu:3,compuat:356,comput:[],computation:[3,6,215,216,326,377],computational:490,compute_arrai:8,compute_fep:[199,415],compute_group_group:231,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[120,300],compute_scalar:8,compute_temp:8,compute_ti:199,compute_vector:8,compute_xrd:167,concaten:[2,3,498],concav:335,concentr:[71,393],concept:[6,148,158,206,478],conceptu:[3,6,71,156,218,220,365,387,402,419,474],concern:[6,73,87,192,232],concetr:71,concis:[11,325],conclud:12,concret:8,concurr:[9,16,356,495],conden:[326,453,455],condens:[6,150,326,372,389,393,407,458],condit:[],conducit:6,conduct:[],cone:472,confer:422,confid:[3,483],config:[12,191,466],configfil:219,configur:[1,2,6,12,15,17,38,59,124,170,188,190,191,193,197,218,219,220,221,225,231,238,239,269,282,290,325,353,363,365,372,377,394,419,422,451,453,455,458,464,469,471,472,483],confin:[469,483],conflict:[3,12,40,424,467],conform:[3,6,13,59,217,218,254,298,303,325,349,365,395,481],confus:[3,458],conjuct:391,conjug:[7,8,239,362,395,432,433],conjunct:[6,7,71,86,87,116,151,156,162,168,172,194,198,199,239,242,246,269,285,286,290,291,292,294,299,314,322,329,334,355,356,365,378,380,384,387,391,395,401,407,424,427,435,456,469,472,476,490,499],connect:[3,6,87,153,171,217,236,284,299,302,311,365,388,399,449,455,466,467,473,490],conput:3,consecut:[3,11,12,39,71,168,194,198,199,221,236,237,387,407,411,464,470,472],consequ:[1,6,204,326,406,483],conserv:[3,29,197,204,217,224,225,232,235,239,241,242,246,251,253,255,269,299,302,317,318,322,329,330,334,365,390,391,399,413,440,478,483],consid:[6,9,70,71,78,87,117,150,153,154,171,191,194,198,199,205,207,210,214,216,217,221,243,256,281,299,321,322,325,326,329,356,384,395,402,433,434,440,449,464,465,467,470,471,472,474,477,479,487,490,495],consider:[6,8,239,240,317,318,319,370,478],consist:[3,6,8,9,11,12,40,42,65,69,79,93,105,110,113,114,117,148,151,153,168,180,190,195,200,201,206,220,221,224,226,229,232,239,240,241,252,255,257,258,259,260,261,262,263,264,265,267,268,269,270,272,273,274,275,276,277,278,286,289,294,296,298,299,317,318,319,320,330,355,356,358,364,365,370,372,377,379,385,387,395,398,402,416,417,419,422,424,434,437,439,440,452,459,467,469,470,471,472,473,474,481,490,495],consistent_fe_initi:203,consit:299,constant:[],constitu:[3,6,245,299,331,335,385,434],constitut:[437,439],constrain:[3,6,8,145,146,147,148,149,151,154,155,156,157,158,160,161,197,206,221,231,232,237,245,249,284,285,297,299,302,312,322,329,363,364,395,474,481,490],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,92,108,120,142,167,218,255,281,298,335,366,370,390,422,424,449,451,452,472,473,488,495],constructor:[8,11],consult:433,consum:[1,294,428,495],consumpt:353,contact:[],contact_stiff:[436,438],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,118,120,142,148,156,166,167,168,170,174,176,187,188,191,193,194,195,197,198,199,203,205,206,207,209,210,211,212,214,219,221,226,233,237,238,239,242,253,269,280,281,284,285,287,289,292,296,299,300,304,314,321,325,326,335,336,339,354,356,364,365,368,369,371,372,373,377,386,387,390,393,394,395,402,403,419,422,426,430,431,432,433,441,451,452,453,454,455,456,458,464,465,466,467,469,470,471,472,474,476,478,481,483,486,487,490,495,497,499],content:[12,18,433,485,487],context:[3,6,8,12,17,118,119,194,215,216,221,284,296,330,362,461,469,476,485,494,495,496],contibut:70,contigu:466,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,104,105,164,194,197,198,199,204,206,207,208,209,210,211,212,214,217,218,219,220,221,231,232,233,235,236,237,239,240,241,247,252,253,255,257,258,259,260,261,262,263,274,275,276,277,278,283,285,288,289,299,300,303,313,314,316,323,324,326,332,335,339,354,369,370,377,391,392,409,412,432,433,434,437,439,454,464,467,469,471,472,477,483,486,487,495,497],continuum:[6,7,9,203,326,437,439],contour_integr:203,contract:[59,218,220,255,286,299],contradictori:3,contrain:302,contraint:269,contrari:[233,240],contrast:[1,6,42,55,64,150,153,220,337,437,439,461,498],contrib:326,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,94,103,105,107,109,110,111,112,114,116,119,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,199,204,205,206,207,209,210,211,212,218,231,239,242,245,246,250,256,276,277,284,285,293,296,299,300,302,328,355,363,365,373,391,392,393,395,402,416,417,422,424,432,433,440,481,487,490],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,87,91,124,142,177,191,193,197,203,204,214,218,219,220,235,236,239,240,255,257,258,259,260,261,262,263,286,291,299,305,306,317,318,319,326,330,353,355,367,395,398,422,432,433,436,438,451,455,464,466,478,484,485],control_typ:203,controlfil:433,convect:91,conveni:[6,12,29,191,195,212,300,358,441,495],convent:[3,8,9,29,179,186,187,194,298,311,338,393,395,495],converg:[3,6,41,88,191,193,195,200,214,217,218,226,229,260,289,291,294,298,302,361,362,363,365,386,387,407,440,464,476,483],convers:[3,8,142,193,194,204,207,286,355,387,388,389,395,407,411,415,427,467,483,494],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,168,175,191,193,194,212,253,337,340,342,346,349,358,365,371,393,422,453,455,462,467,469,470,471,476,486,490,494,495,497,499],convex:[42,335,376],convinc:[7,12],cook:9,cooki:7,cool:[7,158,235,297],cooordin:191,cooper:[5,7],coord123:116,coord1:[3,116,206,210,211],coord2:[3,116,206,210,211],coord3:[3,116,206,210,211],coord:[],coordb:440,coordbb:440,coordiat:363,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,94,104,105,107,115,116,118,136,142,151,157,163,165,166,168,172,190,191,192,193,194,195,197,200,205,206,209,210,211,214,215,216,217,218,219,220,221,224,226,227,229,231,234,235,236,237,238,239,240,252,254,255,257,258,259,261,262,263,276,279,280,281,284,285,286,296,297,299,301,302,303,308,311,312,313,314,316,324,325,326,333,334,336,337,358,363,364,365,370,371,372,375,376,394,440,464,469,470,471,472,474,477,479,483,490,495,496],coordn:[116,206],coorind:[],copi:[0,3,4,8,11,12,15,17,40,121,193,326,365,384,432,467],copper:462,coproccesor:16,coprocessor:[1,4,7,9,16,17,370,482],coproprocessor:17,copy_arrai:8,copyright:[7,8,284],coral:194,core:[],core_shel:150,coreshel:[6,9,380,387,389],cornel:[6,174,481],corner123i:115,corner123x:115,corner123z:115,corner1i:115,corner1x:115,corner1z:115,corner2i:115,corner2x:115,corner2z:115,corner3i:115,corner3x:115,corner3z:115,corner:[3,6,40,115,193,335,336,358,457,469],cornflowerblu:194,cornsilk:194,corpor:16,corr:386,correct:[3,6,9,11,12,16,17,59,87,88,103,104,112,118,150,155,162,193,220,231,233,239,255,256,276,284,286,289,325,331,335,355,365,371,372,373,374,375,376,377,378,379,380,381,382,383,385,386,387,388,389,390,391,392,393,394,395,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,427,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,457,458,460,461,462,469,484,487,490],correction_max_iter:203,correctli:[3,8,9,11,17,71,81,103,104,105,145,146,147,149,151,153,154,155,156,157,160,161,164,191,194,200,221,226,229,240,249,255,256,292,299,302,311,313,332,335,365,366,370,389,417,422,466,467,469,479,494,496],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,42,43,44,45,46,47,48,49,51,53,54,56,70,71,87,97,98,111,114,115,116,117,120,121,129,132,133,134,135,136,138,139,140,142,145,146,155,162,167,174,175,176,177,178,179,180,182,183,185,186,188,191,193,194,198,199,200,206,208,209,210,211,213,216,218,220,227,229,230,234,239,242,243,251,252,253,255,257,258,259,260,261,262,263,264,265,269,272,274,275,276,278,281,282,286,291,299,301,302,317,319,321,330,331,332,334,335,336,338,340,341,342,343,345,346,349,351,356,360,362,364,365,371,372,374,378,379,380,381,382,383,384,385,386,387,390,391,393,394,395,396,397,398,399,400,401,402,405,407,408,409,410,411,412,413,414,415,416,419,420,422,424,425,426,427,429,430,432,433,434,435,440,441,442,451,452,453,454,455,457,458,460,461,462,464,466,467,469,470,472,482,483,484,486,487,490,495],correspondingli:[416,417,478],cosin:[],cosineshift:27,cosmo:[233,238],cossq:[],cost:[1,6,10,11,12,17,39,41,71,111,120,143,167,193,194,206,210,211,214,215,216,228,255,291,326,355,356,368,387,407,411,422,424,451,466,478],costheta0:[451,453,455,458],costheta:430,costli:[11,88,233,366],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,94,105,107,111,114,116,148,158,163,165,181,191,193,194,198,199,206,207,210,214,220,229,238,288,289,290,294,297,299,301,314,315,321,325,326,327,331,335,337,339,347,352,354,361,363,366,370,373,397,401,402,432,433,465,466,467,469,471,473,476,477,485,490,495,496],coulomb:[3,5,6,7,8,9,10,12,14,15,18,72,88,109,110,118,143,169,173,290,292,327,355,356,363,370,378,380,381,382,383,386,387,388,389,390,395,399,400,402,407,411,415,418,424,427,432,433,435,440,450,455,456,458,461,474,481,487,490,494],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,41,63,68,77,91,116,118,119,156,166,172,200,201,204,206,209,210,211,213,214,221,226,228,231,237,255,269,285,302,317,318,335,356,363,364,365,367,370,397,401,424,487,495],counter:[332,464,475,477,483],counteract:231,counterbal:235,counterbalanc:29,counterpart:[191,299,464],counterproduct:18,coupl:[],courant:304,cours:[3,8,128,130,162,191,198,199,232,298,311,325,331,333,334,336,337,356,416,442,466,469,482,490,495,497],courtesi:358,cov:440,coval:[6,29,395,419,440,490],covari:233,cover:[6,71,188,194,203,242,395,405,457],coverag:[71,210],cpc:238,cpp:[1,3,6,8,9,11,12,13,87,191,198,199,229,302],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,194,208,224,240,327,353,356,370,384,450,464,482,483,486,487,488,495],cpuremain:487,cr2:167,cr3:167,crack:[4,366],crada:[5,7],crai:[5,7,13,18,191],crash:[3,12,366,490],craympi:370,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:203,create_faceset:203,create_group:192,create_nodeset:203,createatom:[],creation:[],crimson:194,critchlei:284,criteria:[3,118,169,193,194,215,216,217,250,363,429,457,471,474,495],criterion:[12,41,123,166,168,171,204,214,217,231,269,291,304,332,337,363,365,386,395,399,440,474,483,484],criterioni:483,critic:[6,48,49,253,321,326,363],crmax:71,crmin:71,cross:[3,12,22,71,89,146,176,191,193,205,210,216,220,252,254,276,299,307,311,313,322,329,341,358,365,382,391,392,393,400,401,402,407,409,411,430,435,437,439,453,455,462,469,473,479,497],crossov:1,crossterm:469,crozier:[0,7,13],crucial:289,crystal:[4,6,13,73,108,280,281,324,358,366,473,487,490],crystallin:[6,104,281,358,454,490],crystallis:321,crystallogr:[120,167],crystallograph:[358,487],crystallographi:[120,167,358],cs1:167,cs_chunk:6,cs_im:[40,469],cs_re:[40,469],csanyi:[142,431,441],cscl:419,csequ:6,csh:[11,12,384],cshrc:[11,12],csic:[394,451,453,455,458],csinfo:6,csisi:[394,451,453,455,458],csld:[],cst:393,cstherm:6,cstyle:466,csvr:[],ctcm:[371,393],ctemp_cor:224,cterm:303,ctr:9,ctype:11,cu1:167,cu2:167,cu3au:419,cube:[6,41,166,171,214,224,335,358,490],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:377,cummul:[3,6,212,215,216,217,219,228,233,239,241,314,317,318,319,320,322,329,401,487],cumul:[6,204,206,209,210,211,225,231,239,253,255,260,269,299,300,365],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,103,104,110,118,119,132,143,148,156,158,164,166,169,172,190,191,192,193,194,195,198,199,203,206,210,211,212,214,215,216,217,218,219,220,221,225,226,229,231,233,236,237,239,245,252,255,256,261,262,263,269,274,275,276,278,284,290,291,293,296,297,298,299,302,303,304,305,306,307,308,310,312,313,314,317,318,319,325,326,329,330,331,332,333,334,336,337,339,353,354,355,356,359,360,362,363,364,365,370,376,377,384,386,390,393,395,396,399,402,403,406,416,417,419,420,421,424,430,432,433,436,437,438,439,442,453,455,456,459,464,465,466,467,469,470,471,472,473,475,476,477,479,481,483,484,486,487,495,496,497,498,499],curv:[6,168,231,281],curvatur:[398,434,462],custom:[],cut0:467,cut1:478,cut2:478,cut:[],cuthi:[280,292],cutinn:[379,416,417],cutlo:[280,292],cutmax:430,cutoff1:[383,390,407,411,415,418,427,435],cutoff2:[378,380,381,383,389,390,407,411,415,418,427,435],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,87,92,108,110,117,118,142,166,169,171,216,217,222,280,289,290,292,294,296,299,314,327,331,335,337,353,355,356,363,366,367,368,370,371,372,373,374,375,376,377,378,379,380,381,382,383,385,387,388,389,390,391,392,393,394,395,396,397,398,400,401,402,403,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,432,433,434,435,440,441,442,443,444,445,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,467,471,474,478,490,495],cutoff_glob:376,cutoff_inn:376,cutoffa:394,cutoffc:394,cuu3:393,cval:167,cvd:321,cvel:303,cvff:[],cwiggl:[3,252,331,334,336,495],cyan:[2,193,194],cycl:[3,231,253,255,256,260],cyclic:[3,188],cygwin:12,cylind:[3,4,71,193,206,237,285,332,335,472],cylindr:[6,237,311,332],cypress:370,cyrot:377,cyrstal:281,d3q15:242,d3q19:242,d_double_doubl:15,d_e:326,d_flag2:288,d_flag:288,d_name:[115,191,288,316,479],d_single_doubl:15,d_single_singl:15,d_sx:288,d_sy:288,d_sz:288,daan:324,dai:12,daili:12,daivi:276,damag:[],dammak:294,damp:[3,6,197,202,239,240,241,246,255,256,260,286,289,290,294,299,317,318,330,332,333,362,363,365,378,380,382,387,390,395,399,407,415,427,435,450,456,483,490],damp_com:240,damp_drud:240,dampen:[299,490],dampflag:[332,399],dan:17,danger:[3,12,231,337,391,487],dangl:171,daniel:9,darden:[356,390],darkblu:194,darkcyan:194,darken:193,darkgoldenrod:194,darkgrai:194,darkgreen:194,darkkhaki:194,darkmagenta:194,darkolivegreen:194,darkorang:194,darkorchid:194,darkr:194,darksalmon:194,darkseagreen:194,darkslateblu:194,darkslategrai:194,darkturquois:194,darkviolet:194,dasgupta:290,dash:[399,486],dat:[6,91,188,203,465],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,300],dataset:300,datatyp:3,date:[0,6,12,13,190,432,433,495],datom1:117,datom2:117,datom3:117,datom4:117,datum:[3,6,42,65,68,69,79,93,110,117,191,207],davenport:418,davi:331,david:[9,19,355,356,453,455],daw:[393,430],dbg:14,dcd:[3,6,7,191,192,193,194,195,282,470,474],ddim:190,deactiv:415,dealt:238,debug:[6,7,11,12,13,14,17,120,124,167,168,282,287,353,355,370,403,424,459,467,468,476,479,486,495],deby:[],decai:[92,387,462],decid:[3,6,12,16,71,252,288,299,327,484],decipher:358,declar:192,declin:314,decod:193,decompos:[87,441],decomposit:[3,5,7,18,62,203,282],decoupl:[6,490],decreas:[3,191,200,201,208,217,220,226,229,231,239,325,355],decrement:303,deepli:352,deeppink:194,deepskyblu:194,def:[12,13,467],defaul:61,defect:[6,70,166,422],defgrad:2,defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,174,175,176,177,178,179,180,182,183,185,186,187,188,189,190,191,192,193,194,197,198,199,200,201,202,203,204,205,206,207,209,210,211,212,213,214,215,216,217,218,220,221,224,225,226,229,230,231,234,237,238,239,240,241,242,250,252,254,255,256,257,258,259,260,261,262,263,265,266,267,270,272,273,274,275,276,277,278,280,281,282,284,285,286,288,290,292,297,299,300,301,302,304,308,312,314,316,317,318,319,320,322,323,324,326,328,329,331,332,333,334,335,336,337,339,340,341,342,343,344,345,346,349,350,351,353,355,356,358,360,362,363,364,365,366,367,368,369,370,372,373,374,375,376,378,379,380,381,382,383,384,385,387,388,390,391,392,394,395,397,398,399,400,401,402,403,405,407,408,409,410,411,412,413,414,415,416,417,418,422,423,424,425,426,427,429,430,432,433,434,435,436,437,438,439,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,466,467,469,470,472,473,474,475,478,479,480,481,483,484,486,487,490,491,492,493,494,495,496],definit:[2,3,6,8,12,13,78,80,118,142,194,206,207,208,209,210,211,212,220,237,260,300,316,328,331,334,336,338,350,353,364,373,377,385,395,405,430,437,439,441,457,467,469,471,478,480,494,495],defint:487,deform:[],deg2theta:167,deg:490,degener:[3,284],degrad:[8,18,281,356,478],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,92,93,95,97,98,100,102,103,108,114,145,146,147,148,149,150,151,152,153,154,155,156,157,158,160,161,167,168,174,175,178,179,186,188,190,193,206,217,224,231,233,234,239,240,245,255,256,260,261,262,263,274,275,276,278,282,284,298,299,302,317,318,319,324,340,342,346,349,351,363,390,393,401,479,487,490,496],degress:[148,206],del:483,delai:[3,6,12,366,392,487],deleg:402,delet:[2,3,7,8,12,54,57,60,63,166,171,172,197,206,207,209,210,211,212,215,217,228,231,255,300,317,318,337,339,354,364,366,369,424,449,469,470,471,472,480,481,486,491,493,495,496],delete_atom:[],delete_bond:[],delete_el:203,deli:190,delimit:[467,495],deloc:[256,395,440],delr:419,delt_lo:483,delta:[],delta_1:377,delta_3:377,delta_7:377,delta_conf:3,delta_ij:[419,430],delta_mu:3,delta_pi:377,delta_r:430,delta_sigma:377,delta_ua:376,delx:190,delz:190,dem:376,demand:294,demo:11,demon:279,demonstr:[289,419],den:285,dendrim:401,denniston:[9,242,244,245,246,281],denomin:[7,173],denot:[120,224,240,281,292,294,387,400,402,433,437,439],dens:[71,217,395],densiti:[3,6,7,9,18,40,41,59,101,118,128,142,154,166,168,198,199,203,206,210,211,214,220,229,242,245,248,249,281,285,286,290,326,331,358,360,364,371,377,393,419,420,421,430,434,440,444,446,447,448,469,478,479,487,494],density_continu:439,density_summ:439,depart:[0,7],departur:[253,289],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,93,104,110,111,114,115,116,117,121,142,145,151,155,156,162,168,169,174,175,176,177,178,179,180,182,183,185,186,187,188,190,191,193,194,197,198,199,200,201,204,206,208,209,210,212,213,214,216,218,220,226,227,230,233,234,235,237,239,240,242,244,245,252,255,257,258,259,260,261,262,263,264,265,272,274,275,276,278,280,291,294,296,299,301,302,308,314,317,318,319,321,323,325,326,328,330,331,334,335,336,337,339,340,341,342,343,345,346,349,351,356,358,363,364,366,367,368,370,371,372,374,375,377,378,379,380,381,382,383,384,385,386,387,388,390,391,393,394,395,396,397,398,399,400,401,402,405,407,408,409,410,411,412,413,414,415,416,419,420,422,423,425,426,427,429,430,432,433,434,435,440,441,442,450,451,452,453,454,455,456,457,458,460,461,462,464,466,469,471,472,475,479,481,483,486,487,489,495,496],dependend:6,depflag:12,dephas:[464,483],depos:221,deposit:[],deprec:[290,432],depth:[51,146,193,326,398,434],dequidt:9,der:[87,109,385,386,415,432,433,461,490],deriv:[6,7,8,9,38,56,63,87,142,162,188,207,218,220,231,239,252,255,257,258,259,260,261,262,263,280,286,290,294,323,324,326,331,332,335,362,364,372,377,385,390,395,396,400,409,413,414,419,422,432,433,450,452,461,490],derjagin:461,derlet:280,descend:194,descent:[7,362],descib:[40,193,290],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,112,115,118,120,132,142,143,146,147,148,152,153,156,159,161,162,166,167,168,170,171,180,185,188,191,192,197,198,199,206,207,208,209,210,211,212,214,217,218,219,220,221,223,224,232,233,236,237,238,239,240,241,242,244,245,246,250,254,255,256,260,268,277,280,282,287,288,289,290,291,292,299,303,311,314,315,316,317,318,319,320,321,322,323,324,329,331,332,334,339,355,356,358,361,362,363,364,365,369,372,373,375,376,378,379,380,382,383,384,385,386,387,390,393,395,396,398,399,400,402,407,408,409,410,411,412,413,414,415,416,417,418,419,422,423,429,430,431,432,433,434,435,440,441,442,449,450,451,452,453,454,455,456,458,460,461,462,464,466,467,469,470,471,472,473,479,482,483,486,495,496,497],descript:[],descriptor:[142,191,403],deserno:356,design:[0,3,6,7,8,9,11,13,14,15,17,120,150,153,167,203,217,223,224,255,256,280,281,300,321,326,373,374,375,376,379,382,387,389,395,415,416,417,420,421,430,433,452,478],desir:[2,3,6,7,11,12,14,15,16,33,40,50,59,71,88,91,114,119,143,150,168,181,190,206,212,218,220,229,231,232,239,240,241,245,255,276,284,285,286,287,290,294,299,302,314,317,318,319,320,325,332,347,352,355,356,358,361,363,364,365,391,393,401,416,417,451,453,455,465,466,467,469,473,478,483,484,486,487,495,496,497],desk:7,desktop:[4,6,7,10,12,193],despit:490,destabil:377,destre:349,destroi:[11,39,215,216],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,94,103,105,107,109,111,113,114,116,119,121,142,143,145,146,147,148,151,161,162,163,165,168,169,172,173,176,187,190,191,193,194,197,198,199,203,206,207,208,209,210,212,214,216,217,218,219,220,221,229,231,232,233,234,236,237,239,241,242,246,252,253,254,255,256,257,258,259,260,261,262,263,267,269,274,275,276,277,278,281,284,285,286,288,289,291,292,293,299,302,314,317,318,319,320,321,322,324,325,326,327,328,329,330,337,339,341,350,355,356,359,363,364,366,367,370,371,372,373,375,376,377,379,381,382,383,384,385,386,387,390,391,395,396,398,399,400,401,402,405,407,408,409,410,411,412,413,414,415,416,417,418,419,423,424,429,432,433,434,440,441,442,450,457,460,461,467,469,470,471,472,474,475,478,479,481,484,487,488,495,496,499],detect:[2,3,12,42,61,63,86,92,230,285,325,365,386,401,406,464,466,469,480,483,495],determ:370,determin:[1,3,6,8,9,12,15,39,40,42,51,57,58,59,61,62,68,71,87,103,109,111,114,120,121,129,143,156,157,166,167,168,190,191,193,194,195,196,200,201,202,205,206,207,208,209,210,211,212,213,214,218,220,221,224,226,231,234,235,237,239,240,245,250,252,253,255,261,262,263,274,275,276,278,280,282,286,289,296,297,298,299,300,301,304,306,308,314,317,318,319,321,327,328,331,332,333,334,335,336,337,350,355,356,358,364,366,367,370,372,373,381,386,390,392,393,397,399,402,403,411,419,422,424,433,434,440,449,452,456,461,466,469,470,472,474,476,479,483,485,486,488,494,495,496],detil:110,devan:[9,435],devanathan:455,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,236,260,284,289,290,293,372,377,395,421,422,440,458,471],devemi:9,deviat:[253,260,280,397],deviator:9,devic:[1,3,12,15,17,236,370],device_typ:370,devin:[291,386],devis:421,dfactor:193,dff:490,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,356],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,293,422],dhi:[59,190,220,285],dhug:[253,289],dhugoniot:[253,289],dia:419,diagnost:[],diagon:[3,6,83,142,143,144,218,255,286,299,329,437,439],diagonalstyl:441,diagram:[41,120,167,187,214,282],diallo:401,diam:[193,194,285,364],diamet:[3,6,40,42,115,168,191,193,194,198,199,239,285,299,314,316,330,332,364,376,385,398,399,405,409,434,457,461,469,470,479],diamond:[358,395,419],diamter:[40,285],dick:6,dicsuss:252,dictat:[204,253],did:[3,12,363,391,392,393,399,424,453,455,477],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,164,328,355],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,87,92,95,97,98,122,142,145,146,147,148,149,151,154,155,156,157,158,160,161,162,168,169,171,176,187,188,190,191,193,194,197,199,202,204,206,209,214,215,216,217,218,219,220,224,230,231,232,233,234,235,236,239,240,242,252,255,256,257,258,259,261,262,263,265,267,270,272,273,274,275,278,280,282,284,286,289,290,291,294,297,299,302,303,311,312,314,317,318,319,322,323,324,326,329,330,331,332,335,339,340,350,352,354,355,356,358,359,361,362,364,365,367,368,369,370,371,372,377,381,382,384,385,386,391,393,395,398,399,400,402,405,407,408,410,411,418,419,420,421,423,424,426,430,432,433,434,435,436,437,439,440,441,442,450,451,452,453,455,457,458,461,463,464,466,467,469,471,472,473,474,477,478,479,481,483,484,486,487,488,490,494,495,496,497],differenti:[1,3,6,29,188,355,387,430,454],difficult:[218,282,370,401,478],difficulti:[92,108,302,432],diffract:[],diffus:[],digit:[2,3,194,339,422],dih_table1:188,dih_table2:188,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:216,dihydrid:395,dij:302,dilat:[],dim1:3,dim2:3,dim:[3,59,71,145,149,150,151,154,155,156,157,158,160,168,190,210,220,237,332,358,419,472,494,495,496],dimdim:495,dimems:281,dimens:[],dimensinon:71,dimension:[3,39,92,114,120,142,145,148,149,150,151,154,155,156,157,158,160,167,189,206,210,254,281,326,358,361,365,430,469,479],dimensionless:[106,123,124,126,129,131,133,138,142,326,356,441,461],dimentionless:137,dimer:[6,299,419],dimgrai:194,dimstr:[41,214],dinola:[286,317],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,191,316,490],dir1:480,dir2:480,dir:[1,3,4,8,9,11,12,253,280,289,313,430,432,433,467,480,495],dirac:142,direc:430,direct:[],directli:[3,6,8,9,11,12,87,115,142,144,191,192,193,200,226,233,237,242,281,300,318,330,332,333,334,335,358,362,370,371,372,378,380,381,387,390,393,395,407,411,424,427,435,449,467,479,480,481,487,495],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,60,195,219,238,284,290,293,310,314,323,324,365,369,371,372,377,384,386,387,393,394,396,403,404,415,419,420,421,422,426,430,431,432,433,440,441,451,453,454,455,458,467,469,470,471,480,495],disabl:[3,12,16,326,406,467,482,495],disadvantag:[6,214],disallow:[191,220,255],disappear:471,discard:[2,3,41,71,208,210,214,327,335,466,471,472],discontinu:[9,188,363,413],discourag:419,discov:[13,327],discret:[6,8,40,42,193,194,239,242,376],discuss:[],disk:[6,84,85,92,161,189,221,231,285,467],disloc:[70,422],disord:[39,70,422],disp:[],dispar:434,disperion:[390,411],dispers:[3,6,7,9,166,281,355,356,381,390,411,416,424,433,452,458],displac:[],displace_atom:[],displace_box:59,displacemet:472,displai:[11,13,22,37,44,55,176,187,191,193,341,350,384,450],dispters:3,disregard:422,dissip:[6,232,239,281,323,324,379,391,399,416,417,450],dissolut:215,dist:[6,69,91,110,119,191,282,298,392,449,464,496],distanc:[],distinct:[6,224,296,355,434],distinguish:[6,86,142,245,376,395,468],distort:371,distrbut:371,distribut:[],distro:[113,384,429,430],ditto:[8,12,14,15,16,17,18,42,117,216,462,467],div:8,divd:119,diverg:[3,12,39,299,324,471,490,497],divid:[3,6,16,41,91,114,119,128,130,143,165,166,176,187,194,206,207,209,214,220,280,322,329,334,355,363,365,396,433,440,458,478,486,495],divis:[6,242,377,405,415,466,487,495],dl_poli:[6,7],dlambda:162,dlammps_async_imd:236,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,193],dlammps_gzip:[3,12,191,193,325,469,470,474],dlammps_jpeg:[3,12,193],dlammps_longlong_to_long:12,dlammps_memalign:[12,16],dlammps_png:[3,12,193],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,191],dlen:479,dlmp_intel_offload:[12,16],dlo:[59,190,220,285],dlopen:6,dlvo:[7,385,461],dm_lb:242,dmax:[314,361],dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,42,55,57,59,63,66,68,75,87,90,94,103,105,106,107,109,111,113,114,116,119,121,143,146,147,148,161,163,165,168,169,170,176,187,190,191,192,193,194,195,197,198,199,204,205,206,207,208,209,210,211,212,221,231,239,240,250,255,256,261,262,263,267,274,275,276,277,278,285,288,299,311,314,317,318,319,328,332,335,337,339,341,350,354,363,364,365,370,371,372,375,376,384,386,387,393,394,396,401,402,404,405,419,420,421,424,426,429,430,431,441,450,451,453,455,457,458,467,469,470,471,472,474,477,478,479,486,487,495,496,497,498],docuement:434,dodd:[42,376],dodgerblu:194,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,33,38,39,41,42,50,54,56,59,62,63,67,70,71,72,87,88,91,105,112,118,119,120,144,146,148,150,151,156,158,162,167,168,169,170,172,174,176,181,187,188,190,191,192,193,194,197,203,204,206,210,213,214,216,217,218,220,224,226,228,231,232,235,237,239,240,242,245,251,255,256,257,258,259,261,262,263,274,275,276,277,278,286,287,288,292,294,297,299,314,317,319,321,322,326,329,330,331,334,335,336,337,342,343,344,346,347,349,354,355,356,357,358,364,365,366,371,372,373,374,375,376,377,379,381,382,383,385,386,387,388,390,391,392,393,394,395,397,398,399,400,402,403,404,405,406,409,410,412,413,414,416,417,419,420,421,422,424,430,431,432,433,434,436,437,438,439,440,441,442,443,444,445,446,447,448,449,451,452,453,454,455,456,457,458,460,461,462,464,465,466,467,469,470,471,472,473,476,477,479,480,481,482,483,486,487,490,495,499],doegenomestolif:7,doesn:[3,7,8,12,168,191,204,210,211,311,364,366,370,372,386,394,404,432,433,451,453,454,455,458,469,471],dof:[3,8,114,146,147,148,161,206,299,496],dof_per_atom:[148,206],dof_per_chunk:[148,206],doff:[364,469],doi:[6,219],domain:[3,6,7,12,13,18,39,41,42,58,61,62,71,120,157,167,170,190,192,193,194,197,204,214,218,220,221,235,238,242,255,256,282,294,299,326,331,332,355,356,365,370,392,424,464,466,469,473,486],domin:[1,395,483],don:[0,8,11,12,13,118,171,200,226,240,288,335,419,440,467,469],donadio:318,done:[1,3,6,7,8,12,14,15,16,17,18,38,39,41,56,59,62,71,162,165,168,171,188,191,193,194,203,204,206,208,209,210,211,212,214,215,216,217,218,220,221,229,231,236,237,239,240,247,255,261,262,263,274,275,276,278,279,281,282,283,288,296,299,300,302,314,317,318,319,321,323,324,337,339,354,355,356,363,365,366,369,370,372,381,393,402,403,404,411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,298,299,301,303,308,310,317,318,319,322,323,324,326,328,329,331,334,336,337,339,354,358,363,365,366,367,369,370,386,391,397,398,401,416,422,423,430,432,433,434,436,437,438,440,441,442,452,457,458,462,465,466,467,469,471,472,476,477,480,483,485,487,495,496],equat:[3,6,7,8,9,91,108,114,120,167,176,187,197,218,224,225,233,239,240,242,245,253,254,255,256,260,276,280,282,289,290,294,302,314,322,326,329,331,332,334,336,349,355,356,385,390,391,395,396,399,404,416,417,419,424,434,437,439,444,445,447,448,462,490],equi:256,equidist:254,equil:[3,290,359,476,499],equilater:479,equilibr:[3,4,5,6,7,9,59,91,168,197,204,207,217,218,231,253,255,256,276,277,289,290,291,292,322,323,324,329,386,387,432,433,465,479],equilibria:329,equilibribum:[215,216],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,151,152,175,177,218,220,231,232,233,240,242,255,260,276,289,290,294,298,302,303,311,314,321,322,324,329,340,342,346,349,386,419,426,440,490],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:203,equival:[6,12,13,29,59,61,126,127,135,140,166,170,194,209,212,218,220,231,239,255,276,286,298,299,334,391,395,440,453,455,469,472,477,478,487,490],equlibrium:6,equliibr:[290,292],er3:167,eradiu:[40,115,395,469],eras:[301,323],erat:[220,417],erc:387,erfc:[387,407,424],erforc:115,erg:494,erhart:[204,393,453,455],ermscal:373,ernst:9,eror:3,eros:419,erose_form:419,erot:[],errata:[453,455],erratum:331,erron:3,error:[],erta:399,ervel:[115,469],escap:[221,490],especi:[8,11,16,156,168,197,204,214,231,289,294,297,298,370,466],espresso:[9,293],essenti:[8,11,12,27,88,130,149,150,151,154,155,156,157,158,160,177,207,260,281,330,356,372,387,407,455,474,487],essex:29,establish:[87,235],estim:[1,3,6,10,12,38,41,56,91,143,203,214,225,253,314,321,355,356,361,424,433,452,483,487],esu:494,esub:419,eta:[6,242,255,289,290,292,330,394,396,398,430,454,458,494],eta_dot:255,eta_ij:430,eta_ji:396,etag:[40,469],etail:487,etap:255,etap_dot:255,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,39,40,42,54,61,68,89,90,91,95,111,112,115,117,143,145,148,149,150,151,152,154,155,156,157,158,160,162,168,170,171,172,181,191,193,194,197,198,203,204,205,206,209,210,211,212,215,216,220,221,229,231,232,239,255,285,296,300,326,327,335,339,354,355,363,364,365,366,368,393,394,402,415,417,422,428,432,433,451,453,455,458,464,467,469,470,471,476,478,479,483,485,486,487,488,490,494,495,497,499],ethernet:18,etol:[363,365,464,483],etot0:289,etot:[6,95,97,98,112,143,154,194,224,240,253,289,486,487],eu2:167,eu3:167,euler:[363,365],eulerian:203,euqat:443,europhi:242,ev_tal:8,evalu:[2,3,9,11,12,38,56,71,87,88,91,109,119,142,144,148,158,166,168,190,191,193,194,198,199,200,201,203,205,206,207,208,209,210,211,212,213,220,226,232,234,235,237,238,239,240,281,287,290,301,304,308,317,318,319,328,331,334,336,337,339,355,356,361,363,370,422,424,430,436,438,440,452,464,465,467,471,472,474,476,477,478,479,483,485,487,495,496],evalut:[339,467],evan:[156,276],evanseck:[6,20,174,382,481],evapor:[],evaul:[8,363],evdwl:[109,432,433,487],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,121,169,170,184,188,191,194,197,198,199,204,205,206,209,210,211,212,214,215,216,218,220,221,224,237,240,253,255,256,281,294,296,299,300,310,314,322,326,329,331,335,337,348,355,361,363,365,370,375,395,396,399,402,424,434,458,459,469,470,472,474,475,476,478,479,481,484,486,487,488,490,499],evenli:[3,41,143,188,214,242,405,459],event:[],eventu:[3,6,12,15,170,290,483],ever:[54,56,238,314],evera:[385,398,434,450],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,91,115,121,130,156,171,191,192,193,194,195,197,198,199,200,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,220,221,225,228,229,231,233,235,236,237,242,243,251,255,256,260,279,280,281,285,286,287,288,289,290,291,292,294,296,297,299,300,302,303,314,316,317,318,319,320,321,322,325,326,327,328,329,337,339,354,356,365,366,367,370,391,392,402,415,432,433,440,446,463,464,465,469,471,473,474,476,477,478,483,484,485,487,495,499],everyth:[8,109],everywher:[118,409],eviri:395,evolut:[233,242,282,464],evolv:[242,282,327],ewald:[2,3,5,6,7,8,12,88,112,120,143,327,355,356,363,378,380,381,387,390,395,407,411,427,435,450,452],ewald_disp:390,ewalddisp:3,exact:[22,41,44,71,124,162,171,176,214,217,232,233,239,240,241,285,294,295,314,326,341,355,384,471,476,483,495,497,499],exactli:[3,6,12,14,17,38,41,42,56,59,71,72,91,118,146,152,159,168,188,198,199,209,214,220,225,232,239,240,241,256,268,269,277,281,289,314,319,320,333,370,384,391,393,399,402,405,416,424,452,471,472,479,483,495],exager:490,examin:[6,8,9,17,217,281],examp:[467,495],exampl:[],exce:[3,6,16,17,18,41,58,71,170,205,206,209,210,211,212,214,218,220,225,228,255,281,296,300,305,306,314,363,370,469,495],exceed:[3,41,59,214,220,255,314,477],excel:395,except:[1,2,5,6,8,9,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,71,89,90,110,111,114,119,143,145,146,147,148,149,150,151,152,154,155,156,157,158,159,160,161,168,172,174,175,176,177,178,179,180,182,183,185,186,187,188,190,191,194,197,200,206,207,209,213,214,218,220,227,230,231,234,237,239,241,255,256,257,258,259,260,261,262,263,264,265,268,269,272,274,275,276,277,278,282,291,292,299,301,302,311,314,317,319,320,326,330,334,337,339,340,341,342,343,345,346,349,350,351,355,356,358,360,364,365,366,368,369,370,371,372,374,378,379,380,381,382,383,384,385,386,387,389,390,391,393,394,395,396,397,398,399,400,401,402,405,407,408,409,410,411,412,413,414,415,416,417,420,425,426,427,429,432,433,434,435,442,450,451,452,453,454,455,457,458,460,461,462,464,466,467,469,471,472,474,477,478,479,480,481,483,487,490,494,495,496,498],excess:[208,395],exchang:[2,3,6,8,9,61,62,197,203,204,231,239,291,299,322,326,329,355,370,395,484],exchange:355,excit:[9,395],exclud:[3,6,9,12,16,17,63,71,114,142,148,155,156,172,191,206,210,215,216,243,251,284,297,299,321,332,337,363,364,366,379,399,402,416,417,424,449,481],exclus:[1,3,9,12,16,87,370,386,422,424,478,488],excurs:[255,464],exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,169,193,236,293,339,354,357,369,465,467,477,480,483,495],exempl:440,exemplari:232,exemplifi:395,exert:[6,237,240,294,333,334,335,356],exhaust:[203,369,495],exhibit:[92,255,362,395,478],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,124,168,169,187,192,193,194,197,202,213,216,218,221,231,284,285,287,337,340,342,343,344,346,350,359,364,370,402,432,449,459,465,467,469,470,471,480,481,482,495,496,497],exit:[2,3,11,12,41,57,191,214,354,369,467,468,477,486,495],exlanatori:3,exp:[],expand:[],expans:[12,142,191,480,495],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,103,149,160,166,188,214,226,231,233,252,280,286,288,289,294,299,337,356,366,384,419,422,424,464,467,469,471,474,478,483,495],expens:[6,10,71,194,280,284,299,326,337,355,356,366,370,467],experi:[6,13,15,17,213,221,236,245,254,286,298,299,361,365,391,424,478,483],experienc:[6,12,244,245],experiment:[231,355,370,483],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,93,148,156,188,191,193,194,197,206,207,212,214,216,218,220,255,280,288,299,311,337,339,354,355,358,364,365,369,375,393,405,440,442,457,467,470,471,474,476,479,490,495,499],explan:[3,6,59,115,142,191,206,254,280,402,463,466,467,469,478],explanatori:[3,8,119,191,205,206,209,210,211,299,364,466,495],explantori:[3,295],explic:423,explicit:[6,9,11,22,44,77,87,115,118,162,176,198,199,220,305,306,341,360,372,373,377,382,384,393,395,406,416,456,463,466,470,473],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,111,114,145,155,158,166,168,174,175,177,178,179,180,182,183,185,186,188,191,194,200,210,213,220,227,230,232,234,239,255,257,258,259,260,261,262,263,264,265,272,274,275,276,278,288,289,291,299,301,302,317,319,320,326,330,334,340,342,343,345,346,349,351,364,370,371,372,374,378,379,380,381,382,383,384,385,386,387,388,390,391,392,393,394,396,397,398,399,400,401,402,405,406,407,408,409,410,411,412,413,414,415,416,420,422,424,425,426,427,429,434,435,442,443,444,445,446,447,448,450,451,452,453,454,455,456,457,458,460,461,462,469,471,472,478,479,481,482,488,490],explictli:[16,482],exploit:[9,15,17,282],explor:[120,167],expon:[3,290,292,393,398,401,415,423,435],exponenti:[87,430,451,458,462,483,495],expos:11,exposit:[203,391,392],express:[6,142,154,168,198,199,218,252,280,290,326,332,339,377,393,395,409,419,440,441,450,495],expressiont:377,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,95,98,99,109,111,119,121,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,197,200,201,204,212,213,219,222,226,229,230,231,233,234,235,237,239,241,253,255,260,269,280,281,297,298,299,301,303,308,311,313,317,318,319,320,321,323,324,326,328,331,335,336,398,419,422,433,434,441,486,487],extent:[1,3,41,42,45,57,71,166,170,191,202,210,214,237,333,336,355,358,372,436,438,452,466,469,472],exterior:[3,6,335],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,103,111,112,114,120,143,145,146,147,149,151,154,155,156,157,158,160,161,167,168,169,170,174,194,209,214,216,255,287,288,289,299,314,363,364,367,368,390,399,402,405,419,424,466,467,469,472,481,490,495],extract:[3,6,11,13,36,63,87,109,117,119,121,198,199,292,365,387,396,419,441,467,474,486],extract_atom:11,extract_comput:[11,467],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,193,208,218,220,255,324,395,454,490],extrema:415,extrins:203,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[164,328],f_a:[453,454,455],f_ave:119,f_c:454,f_f:455,f_fix_id:289,f_harm:324,f_i:[29,430],f_id:[6,71,119,121,191,197,205,206,207,208,209,210,211,212,250,316,328,487,495],f_ij:430,f_indent:212,f_int:323,f_j:29,f_jj:91,f_k:430,f_langevin:326,f_max:[289,294],f_msst:253,f_r:[240,453,454,455],f_sigma:377,f_solid:324,f_ss:6,f_temp:[],face:[3,6,57,59,71,156,166,170,202,210,211,331,333,334,335,336,358,398,419,434,469,472],face_threshold:166,facet:166,facil:[0,12],facilit:[6,13,42],fact:[6,8,16,233,314,324,399,440,481],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,72,87,91,103,110,117,118,120,142,162,167,170,174,185,190,191,193,194,198,199,207,214,218,220,221,231,236,239,241,242,253,255,256,260,282,286,290,298,302,304,306,314,318,322,329,330,331,335,346,356,358,364,370,372,373,377,378,380,382,387,388,389,391,395,399,402,406,407,419,422,424,426,427,433,435,442,451,456,466,469,472,473,478,481,483,484,487,490,494,495],factori:[3,467],factoriz:355,fail:[3,11,12,59,172,218,221,355,363,365,389,433,467],failur:[123,437,468,495],fairli:[11,424,478,483],faken:73,falcon:236,fall:[3,6,194,209,285,467,495],fals:[86,337,339,440,495],fame:8,famili:[458,466],familiar:[0,11],fan:430,far:[3,6,12,17,57,59,61,86,191,194,195,214,215,216,218,221,255,280,298,299,314,331,342,346,361,365,366,457,467,469,474,487],farago:239,farrel:[453,455],farther:191,fashion:[6,8,41,71,168,194,197,198,199,204,210,214,216,221,231,233,237,252,253,255,257,258,259,260,261,262,263,271,274,275,276,277,278,288,289,291,299,303,307,313,316,324,326,330,331,332,334,336,365,402,416,472,481,495,498],fasolino:404,fast:[6,7,9,12,13,17,39,191,266,289,327,355,356,379,416,417,422,450,452,471,476,478,487,496,499],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,106,111,114,145,155,174,175,177,178,179,180,182,183,185,186,188,191,194,200,213,214,220,227,230,234,238,239,255,257,258,259,260,261,262,263,264,265,272,274,275,276,278,286,290,291,299,301,302,314,317,319,321,323,326,330,334,340,342,343,345,346,349,351,355,356,367,368,370,371,372,374,377,378,379,380,381,382,383,384,385,386,387,390,391,393,394,396,397,398,399,400,401,402,405,407,408,409,410,411,412,413,414,415,416,420,425,426,427,429,434,435,442,450,451,452,453,454,455,457,458,460,461,462,464,472,478,482,490],fastest:[1,6,14,17,156,210,326,327,370,466],fatal:[3,486],fault:[70,433],faulti:12,fava:398,favor:217,favorit:7,fbmc:321,fcc:[],fcm:[271,495],fdirect:224,fdotr:403,fdti:87,fe2:167,fe3:167,fe_md_boundari:203,featu:8,featur:[],fecr:393,feedback:[7,236],feel:[7,236,237,245,280,335,337,365,424],felling:421,felt:335,femtosecond:494,fene:[],fennel:[387,407],fep:[],ferguson:[6,174,481],fermi:[1,12,15,154,370,455],fermion:[9,395],fernando:418,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,39,195,205,206,207,209,210,211,212,240,255,285,288,290,302,328,355,363,364,365,372,440,466,469,474,478,480,488,495,497],fewer:[1,3,11,15,16,61,245,478],fewest:3,fextern:229,feynman:282,fff:467,ffield:[386,396,432,433,440],ffmpeg:[3,12,193],ffplai:193,fft:[1,3,7,12,14,15,88,111,112,143,281,355,356,478],fft_inc:[12,356],fft_lib:12,fft_path:12,fftbench:[355,488],fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],ficiti:449,fictiti:[6,200,201,226,229,233,282,298,387,407,411,449],field1:[470,474],field2:470,field:[],fifth:[311,426],figur:[1,3,8,11,12,289,466,467],fij:390,file0:280,file1:[11,13,280,325,339,364,474,476,480],file2:[11,13,325,339,364,474,476,480],file:[],file_from:192,filen:364,filenam:[3,12,13,38,41,56,188,191,193,194,195,203,206,207,208,209,210,211,212,214,219,280,284,287,290,291,292,295,296,299,300,325,326,352,353,354,364,365,371,372,377,387,393,394,396,404,419,420,421,426,430,431,432,433,440,441,451,452,453,454,455,458,465,466,467,470,471,476,480,487,495,497,498,499],filennam:476,filep:[3,191,194,471,476,499],filepo:296,fill:[7,9,168,193,285,326,358,366,377,422,433,472],filter:[194,203],final_integr:8,final_integrate_respa:8,finchham:[6,150,389],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,119,171,188,195,204,217,218,228,231,254,280,286,294,298,361,363,365,366,387,402,407,411,419,440,450,452,490,495],find_custom:8,fine:[16,17,172,200,226,324,366,370,495],finer:[142,168,495],finest:355,finger:[168,190,252,472],finish:[6,11,41,214,339,352,354,355,367,369,370,457,474,495,496],finit:[],finni:[7,393,450],finvers:224,fiorin:[9,219],fire:[],firebrick:194,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,104,105,106,108,114,118,119,129,132,135,136,140,143,153,156,162,164,166,167,169,170,171,175,188,191,192,193,194,195,197,198,206,207,209,210,211,212,214,217,220,231,232,237,242,252,253,254,255,280,282,287,288,289,291,296,299,302,303,311,312,314,315,316,323,324,325,326,328,332,337,339,340,347,358,363,364,365,366,369,370,371,372,375,377,378,380,382,384,386,387,393,395,396,399,400,402,403,404,406,407,411,416,417,419,421,422,424,426,430,432,433,440,441,449,451,452,453,454,455,458,462,464,465,466,467,469,470,471,474,476,478,481,482,483,486,487,490,495,496,497,499],fischer:[6,9,19,20,174,382,481],fit:[3,6,9,12,38,56,188,298,314,372,377,404,419,424,445,452,454,477,495],five:[73,154,289,364,377,420,469,483],fix:[],fix_adapt:[162,199,415],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,204,285],fix_evapor:204,fix_flux:203,fix_gcmc:[204,364],fix_gl:233,fix_gld:233,fix_grav:285,fix_id:[3,218,253,255,257,258,259,260,261,262,263,286,289],fix_modifi:[],fix_mov:[190,332],fix_nh:8,fix_npt:233,fix_nvt:[204,231],fix_poem:[3,6],fix_pour:[3,221],fix_qbmsst:9,fix_qeq:[3,386],fix_rattl:302,fix_reax_bond:432,fix_rigid:[245,375],fix_saed_vtk:300,fix_setforc:8,fix_shak:302,fix_srd:3,fix_styl:260,fix_temp_rescal:320,fixedpoint:[218,255],fixextern:229,fixid:203,fji:390,flag1:[223,368],flag2:[223,368],flag:[3,8,11,12,14,15,16,17,40,66,74,75,81,86,89,90,94,104,105,107,120,163,167,171,191,193,194,195,212,217,219,223,236,239,243,245,251,252,281,288,299,311,313,314,321,325,334,337,353,356,364,368,369,370,372,401,406,419,422,449,464,466,467,469,470,471,473,474,475,479,495],flag_buck:381,flag_coul:[381,390,411],flag_lj:[390,411],flagfld:[379,416,417],flaghi:[3,379,416,417],flaglog:[379,416,417],flagn:223,flagvf:[379,416,417],flat:[6,326,331,332,336],flavor:[2,7,12],fld:[9,331,379,416,417],flen:373,flex_press:373,flexibl:[3,6,8,169,193,206,210,219,233,256,322,329,395,454,487],flip:[3,6,220,255,333,334],floor:495,flop:12,floralwhit:194,flow:[],fluctuat:[6,64,87,218,231,232,239,242,255,260,280,281,324,326,349],fluid:[],fluid_veloc:246,flush:[3,194,486],flux:[],flv:193,fly:[7,9,12,41,193,197,203,208,221,224,299,302,327,377,422,487,490],fmackai:9,fmag:222,fmass:282,fmax:[363,487],fmomentum:224,fmsec:[2,194,239,240,252,255,286,299,317,318,478,489,494,496],fname:354,fno:[12,16],fnorm:[363,487],fnpt:224,fnvt:224,foce:402,fock:373,focu:302,fogarti:[9,292,433],foil:[142,280,441],fold:[312,478],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,92,97,98,108,115,118,119,121,142,143,146,147,148,154,156,161,164,166,168,169,174,177,178,179,180,182,183,185,186,188,191,192,193,194,197,203,204,205,206,207,208,209,210,211,212,214,219,220,221,224,225,229,231,232,233,236,238,239,240,242,245,253,255,260,261,262,263,274,275,276,278,281,282,284,287,288,289,290,292,294,296,298,299,300,302,316,317,318,319,322,323,324,325,326,328,329,337,338,342,343,344,345,346,349,351,353,358,360,363,364,365,370,371,372,373,374,375,376,377,378,379,380,381,382,383,385,386,387,388,389,390,391,392,393,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,423,424,425,426,427,429,430,431,432,433,434,435,437,439,440,441,442,443,444,445,446,447,448,449,451,452,453,454,455,456,457,458,460,461,462,464,466,467,469,470,472,474,476,477,478,481,483,484,485,490,495,496,498],foo:[4,8,11,12,191,193,229,467,480,495],foot:6,footprint:[12,370],fopenmp:[12,16,18],forc:[],force_uvm:17,forceatom:245,forcefield:[298,401],forcegroup:242,forcezero:361,ford:390,forestgreen:194,forev:71,forget:[240,490],forgiv:255,fork:[12,191],form:[2,3,6,8,12,19,22,44,54,63,66,74,75,77,81,87,89,90,92,94,104,105,107,118,142,143,162,163,172,176,194,197,198,199,216,232,233,239,241,245,252,276,281,292,294,298,299,326,331,335,340,341,344,349,360,362,364,365,372,373,377,384,393,395,397,401,402,406,418,419,421,422,426,427,430,432,433,434,440,441,442,450,452,453,454,455,461,463,466,467,469,474,479,486,490,495],formal:[6,78,80,91,232,233,239,255,282,314,322,440],format:[2,3,6,7,8,9,12,13,22,38,41,44,56,68,77,176,188,191,192,193,194,195,206,209,210,211,212,214,216,281,284,288,290,292,295,299,300,310,325,326,337,338,341,360,364,365,371,372,377,384,393,396,406,419,421,431,432,433,435,441,452,458,459,466,467,469,470,471,474,485,486,487,495,497],former:[6,12,16,39,41,194,214,326,330,377,379,475,481,495],formerli:[7,13],formul:[1,40,64,143,200,226,239,255,276,290,292,298,302,325,355,372,377,393,395,398,419,429],formula:[2,3,6,7,13,21,22,37,44,54,55,70,73,87,89,90,91,95,97,98,107,114,120,143,145,146,147,148,149,150,151,152,154,155,156,157,158,159,160,161,167,168,173,175,176,187,190,191,198,199,200,201,206,207,208,209,212,213,220,226,234,235,237,239,240,252,280,281,287,296,301,308,312,314,317,318,319,328,331,334,336,337,339,340,341,343,350,358,364,372,373,375,377,382,383,384,385,390,391,393,394,398,399,400,401,403,406,407,409,410,411,413,414,416,417,419,423,424,425,434,435,442,450,451,453,454,455,458,460,461,465,469,472,479,486,487,494,495,496],forth:[1,6,11,12,13,14,15,369,467,472,476],fortran:[3,6,9,11,12,13,229,393,402,419,432,433],fortun:8,forward:[3,8,87,354,365,370],foster:[377,429,430],foul:171,found:[3,6,9,12,73,162,191,217,219,231,236,242,281,321,327,339,354,366,384,387,390,464,470,471,486],four:[6,11,54,81,104,105,142,164,253,326,349,364,365,422,464],fourier:[],fourth:[6,106,298,311,321,382,426,440],fox:[6,120,174,448,481],fphi:[38,56,452],fpic:12,fplo:[38,56,452],fprime:452,fqdn:238,fqq:390,frac:[],fraction:[1,3,6,8,12,16,39,41,80,111,143,171,190,193,194,204,215,216,217,218,253,285,289,296,297,314,319,320,358,365,370,377,379,399,416,417,474,479],fragment:[42,236,296],fraig:[42,376],frame:[83,142,194,203,253,289,333,398],framer:[193,194],framework:[5,233,371,441],franc:9,fraunhof:9,free:[5,6,7,9,13,29,60,63,70,87,162,199,280,314,323,324,325,326,362,365,373,395,415,422,430,461,466],freedom:[3,6,8,95,97,98,100,102,103,114,145,146,147,148,149,150,151,152,153,154,155,156,157,158,160,161,206,217,224,231,233,239,240,245,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rnod:245,innner:413,inordin:327,inorgan:[6,458],inp:[219,339,441,458],input1:[65,68,69,79,93,110,115,116,117,119,121,316],input2:[65,68,69,79,93,110,115,116,117,119,121,316],input:[],input_doubl:3,inquir:304,insensit:12,insert:[3,5,7,8,12,59,168,197,221,231,237,285,355,441,449,467,473,490],insid:[2,3,6,8,11,71,131,137,168,191,194,205,210,211,221,222,228,231,237,242,245,285,299,314,331,333,334,335,336,337,353,358,409,467,468,469,471,472,479,483,495],insight:[6,13],instabl:[242,390,439],instal:[],instanc:[6,11,198,219,233,333,397,402,424,430,467,490],instantan:[6,63,217,218,232,233,255,260,281,286,289,294,296,299,321,475,487],instanti:[6,11,12,203,402,466],instead:[1,3,6,8,9,11,12,13,17,18,40,41,59,61,63,70,71,90,104,119,146,150,172,188,191,199,206,209,210,211,212,214,218,219,231,239,242,245,246,281,287,297,299,316,334,353,355,356,359,366,370,380,381,393,406,408,415,419,422,464,472,476,483,485,490,495],institut:[9,236,284],instruct:[],insuffici:[3,6,12],insult:255,insur:[3,6,11,12,17,39,40,61,73,103,105,168,169,188,191,193,194,200,215,216,221,226,227,228,229,231,234,239,251,287,288,297,299,314,326,331,335,336,337,339,354,364,366,370,385,398,402,428,434,452,466,467,469,470,474,477,478,486,487,495,496],int_max:3,integ:[3,6,8,11,12,39,40,42,64,68,70,71,108,115,117,119,121,142,166,168,171,172,174,178,179,183,188,190,191,193,194,204,206,210,211,215,216,217,221,223,229,231,232,233,236,239,240,241,242,281,284,285,288,289,294,299,314,316,318,321,325,326,345,355,358,379,391,392,405,419,432,433,437,439,441,464,466,467,468,469,477,478,479,483,486,495,496],integr:[],integrate_ulsph:[],intel:[],intel_cpu:[12,16],intel_phi:[12,16],intend:[3,6,8,12,13,36,208,232,431,469],intens:[1,3,6,9,63,66,74,75,86,89,90,91,94,104,105,106,107,114,116,118,119,120,121,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,163,164,165,167,197,206,207,209,210,211,212,214,215,216,217,225,228,235,245,253,255,260,296,299,300,314,322,326,328,329,486,487],intepol:495,inter:[14,18,42,61,62,148,171,172,191,217,239,241,254,291,299,355,365,377,479,490,495,497,499],interact:[1,3,6,7,8,9,10,11,12,14,15,16,17,22,29,33,37,39,42,44,50,54,55,57,61,63,65,69,72,77,79,87,88,92,93,108,109,110,112,114,117,118,124,125,126,127,129,130,131,132,133,134,135,137,138,139,140,142,143,144,146,147,161,162,166,169,170,171,172,173,174,176,180,181,187,191,197,198,199,215,216,217,230,231,236,237,239,241,245,269,280,282,284,290,292,298,299,305,306,314,315,321,326,330,331,332,335,336,341,342,343,344,346,350,355,356,363,364,365,366,367,368,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,427,429,430,433,434,435,437,439,440,441,442,449,450,451,453,454,455,456,457,458,459,460,461,462,464,467,469,471,473,474,478,479,481,486,487,490,497],interatom:[3,4,7,168,191,254,323,324,371,377,393,395,403,419,422,440,454,495],intercept:120,interchang:6,interconnect:18,interconvert:395,intereract:39,interesect:335,interest:[1,5,7,8,9,11,13,71,167,282,321,324,356,394,417,432,433,467,495],interf:370,interfac:[],interfer:[12,255,372],interg:[6,490],intergr:[478,482],interi:417,interior:[3,6,41,335,472],interlac:419,interleav:[6,168,477],intermedi:[6,12,59,193,254,280,349,365,467,468,477,481],intermix:464,intermolecular:372,intern:[0,2,3,5,6,9,11,16,20,21,24,28,32,35,36,39,40,42,63,87,100,102,120,143,148,150,167,175,188,193,194,197,198,199,203,216,220,224,236,248,249,253,255,260,281,299,303,340,342,346,349,353,363,364,443,444,452,467,469,471,474,483,486,487,494,495,496,497],internal_element_set:203,internal_quadratur:203,internet:238,interpenetr:419,interpentr:[444,445,447],interpol:[6,15,38,56,101,188,193,194,203,242,280,355,356,365,377,424,433,446,452,453],interpret:[2,6,11,193,209,399,442,464,467,483,495],interrupt:289,intersect:[3,6,120,194,335,337,472],intersert:335,interspers:363,interstiti:[166,422],intertia:[3,94],interv:[3,6,91,192,207,239,255,289,294,295,306,440,446,464,483,495],intestieti:120,intial:[6,370,372],intiial:[41,474],intiti:[3,313],intra:299,intra_energi:231,intramolecular:[29,231],introduc:[6,9,92,108,193,255,289,294,299,349,355,371,387,395,407,411,415,451,483,495],introduct:[],intsal:[],intuit:358,inv:[120,167,300],invalid:[3,12,71,89,171,269,365,416,417,471],invari:[108,135,140,142],invent:302,invers:[],invert:[1,6,172,281],invis:335,invoc:[166,217,370,437,439,467],invok:[1,3,6,7,8,11,12,13,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,59,63,66,71,74,75,81,87,88,89,90,94,104,105,107,111,112,113,114,119,145,155,162,163,166,168,169,171,172,174,175,177,178,179,180,182,183,185,186,188,191,193,194,195,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,220,221,222,223,225,226,227,228,229,230,231,232,234,235,236,237,239,240,241,242,243,244,245,246,247,248,249,251,252,254,255,257,258,259,260,261,262,263,264,265,266,267,26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:[215,216],probab:442,probabl:[3,8,12,40,71,158,171,172,174,204,214,215,216,217,221,231,240,255,285,331,337,363,424,464,483,490],probe:495,problem:[],problemat:231,proc:[1,3,8,11,12,15,115,191,354,466],proce:[41,54,172,214,225,365,422,476,484,487],procedur:[6,12,39,41,194,204,214,231,239,240,241,255,257,258,259,260,261,262,263,274,275,276,277,278,281,317,318,319,320,323,324,363,365,372,379,470,490],proceed:[12,422],procesor:[41,466],process:[],processor:[],processsor:[41,214,466],procp1:191,procsessor:488,procssor:478,produc:[1,3,4,6,7,9,12,13,14,15,16,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,42,43,45,46,47,48,49,51,53,54,56,63,65,68,69,71,79,93,110,111,112,114,115,116,117,119,121,143,145,155,174,175,177,178,179,180,182,183,185,186,188,191,194,197,200,205,206,207,209,210,211,212,213,214,217,220,227,229,230,232,233,234,239,240,241,250,252,255,257,258,259,260,261,262,263,264,265,272,274,275,276,278,285,289,290,291,294,299,300,301,302,315,316,317,319,326,327,328,330,331,334,339,340,342,343,345,346,349,351,356,363,365,368,370,371,372,374,378,379,380,381,382,383,385,386,387,390,391,393,394,395,396,397,398,399,400,401,402,405,407,408,409,410,411,412,413,414,415,416,420,425,426,427,429,430,433,434,435,442,451,452,453,454,455,457,458,460,461,462,464,466,471,472,474,475,478,483,495,496],product:[6,16,17,18,142,220,276,290,327,370,373,395,433,466,495],proessor:370,prof:284,profi:157,profil:[],program:[3,4,6,7,9,11,12,13,17,144,191,193,194,195,197,219,229,236,242,293,393,467,468,480,495],programm:[13,17],progress:[1,41,214,236,253,289,362,363,365,487,490],prohibit:479,project:[6,7,13,14,362,450],promis:7,promot:377,prompt:[8,11,12,236,480],proni:[3,232,233],proofread:8,prop:[6,288],propag:[4,9,202,255,289,304,395,402],propens:6,proper:[217,280,419,467],properati:288,properli:[200,226,299,310,364,365,467,496],properti:[],propoerti:314,proport:[6,39,41,87,104,105,164,214,239,240,241,289,322,329,330,399],proportion:239,propos:[6,142,204,218,231,255,276,294,407,421,454,456],prospect:7,protect:314,protein:[7,10,168,297,299,312,469,477],protocol:236,proton:[455,462,494],prototyp:[10,42,429],prouduc:[212,328],prove:242,proven:276,provid:[1,3,4,6,7,8,9,11,12,13,14,15,16,17,18,29,40,42,61,67,70,120,141,144,162,167,168,192,193,195,205,206,212,217,218,219,220,229,231,236,238,242,246,253,255,281,289,290,293,294,299,303,321,323,324,327,328,339,353,355,356,361,365,370,372,377,379,384,386,387,391,394,395,399,401,404,406,415,416,419,421,422,430,431,432,433,440,441,449,450,451,453,454,455,458,466,471,477,479,482,483,487,488,495],proxim:190,psa:334,pscreen:[3,12,478],pscrozi:[0,7,13],psec:[194,220,235,239,240,255,286,299,317,318,489,494],psend:466,pseudo:[395,464,469,474],pseudodynam:321,pseudopotenti:[9,422],psf:6,psi:[396,461],psi_ij:396,pstart:[3,255,256,260,286,299],pstop:[3,255,256,260,286,299],pstyle:[87,109,198,199],psu:[432,433],psuedo:474,pt2:167,pt4:167,ptarget:218,pthread:[12,17],ptr:[6,11,229,467],ptype1:117,ptype2:117,pu3:167,pu4:167,pu6:167,publicli:5,publish:[7,242,246,290,387,419,422,453,455],pull:[303,311],puls:326,pump:[416,417],punctuat:[2,464,483],purchas:193,purdu:[9,13],pure:[11,314,402,420,421,453,455,478],purg:[3,470],purpl:[2,194],purport:11,purpos:[3,6,7,12,42,61,71,120,130,136,151,152,167,168,170,172,188,191,210,212,217,218,239,280,282,285,287,298,314,355,370,381,405,411,422,424,457,469,472,476,479,481,482,495,499],push:[3,8,200,213,220,237,254,280,297,303,363,399,442],pushd:237,put:[3,6,8,11,12,13,39,59,156,168,191,221,225,333,334,337,358,432,467,469,473],putenv:[480,495],px1:478,px2:478,pxx:[218,255,286,299,355,356,486,487],pxy:[3,6,487],pxz:[3,6,487],py1:478,py2:478,pydir:11,pyi:[218,255,286,299,355,356,487],pymol:[7,11,13],pymol_aspher:[],pympi:11,pypar:11,python:[],pythonpath:11,pyz:[3,6,487],pz1:478,pz2:478,pzz:[218,253,255,286,289,299,355,356,487],q_1:440,q_2:440,q_3:440,q_c:[],q_d:490,q_i:[396,415],q_j:415,qbmsst:[],qcore:290,qdamp:290,qdist:[387,407,411,415],qeq1:290,qeq2:290,qeq:[],qeqal:440,qeqallparallel:440,qfile:[290,387],qin:235,qinitmod:440,qmin:362,qmmm:[],qmol:293,qout:235,qstep:290,qtb:[],quad:[12,18,370,466],quadrat:[],quadratur:[87,203],quadrupl:371,quadruplet:[184,187,340,342,343,344,346,348,349,350],qualifi:[3,238],qualiti:[7,9,193,194],quantic:440,quantit:[74,81,104,105,106,164,399],quantiti:[],quantum:[6,9,142,229,233,282,289,293,294,377,395,422,440,450],quantum_temperatur:289,quartic:[],quartic_spher:203,quartz:[289,294],quasi:282,quat:479,quaternion:[3,6,40,82,115,132,146,147,168,257,258,261,262,265,266,267,274,275,398,469,479],quati:[115,469],quatj:[115,469],quatk:[115,469],quatw:[115,469],queen:13,quench:[337,464,483],queri:[3,11,54,271,467,495],quest:[6,229],question:[8,9,12,13,280,337,429,495],quick:[0,9,12,14,15,16,17,18,19],quickli:[3,4,8,12,13,39,92,214,220,231,236,314,362,363,365],quickmin:[361,362,363,365,483],quicktim:[4,193],quip:[],quit:[],quot:[2,3,12,192,245,287,339,419,464,465,467,477,495],quotat:440,r10:377,r12:398,r_1:142,r_2:142,r_c:[388,390,397,455],r_cu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14,377,457],recust:41,recv:466,red:[2,10,193,194,217,282],redefin:[3,471,477,495],redirect:12,redo:12,reduc:[],reduct:[18,19,119,120,167,253,289,355],redund:396,ree:445,reed:[253,289],rees:[7,9,13],ref:[323,324,362],refactor:6,refer:[],referenc:[3,6,12,63,68,71,116,191,197,207,212,231,288,328,356,387,401,426,434,467,487,495],reflect:[],reformat:7,refresh:203,reg:472,regard:[6,59,252,302,307,429,433],regardless:[15,71,168,171,190,209,210,220,239,255,257,258,259,261,262,263,286,299,308,314,370,466,472,479],regim:[6,322,329,388,478],region:[],region_spher:8,region_styl:335,regist:[8,118,144,310,432,433],regoin:6,regress:495,regspher:168,regstrip:337,regul:6,regular:[1,3,9,41,62,88,166,170,191,204,214,231,326,356,388,466,469,471,473],reigon:495,reinhardt:[323,324],reject:[168,217,432,484],rel:[1,6,14,27,36,41,59,71,92,104,124,132,142,146,150,151,153,168,177,194,197,204,210,214,220,221,224,231,237,240,251,252,276,280,285,294,296,297,303,311,314,316,321,322,326,333,337,355,356,363,395,398,399,416,417,419,434,461,470,478,483,487,490,496],relat:[],relatic:[],relationship:[6,290,339,355,440,461,490,495],relax:[],releas:[0,5,7,8,13,215],relect:[3,424],reles:42,relev:[2,6,12,41,78,80,113,130,168,172,194,198,199,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,220,221,222,225,227,228,230,231,232,235,236,242,243,244,246,247,248,249,251,252,254,264,265,266,267,268,269,270,271,272,273,279,283,284,285,287,288,291,293,295,296,297,300,301,302,303,308,312,314,315,316,321,322,325,326,327,328,329,330,331,332,333,334,336,337,355,363,373,374,379,385,387,388,390,391,392,395,397,398,399,400,401,406,408,409,410,412,413,414,416,417,424,425,429,434,442,449,452,460,461,462,466,482,496],reli:[3,12,291,395,433,462,469,479],reloc:12,remain:[7,12,33,37,41,50,55,59,71,87,105,148,149,150,151,155,156,157,158,160,171,181,187,188,191,198,199,204,206,207,210,211,218,220,239,240,247,255,256,261,262,263,274,275,276,278,283,284,306,314,317,318,319,325,326,337,339,347,350,364,377,395,402,415,422,424,450,464,469,470,474,479,481,483,487,490,495,496],remaina:377,remaind:[168,191,221,285,314,327,455,469],remap:[3,6,12,59,61,71,151,168,190,210,220,237,252,276,355,469,470,471],remedi:[6,490],rememb:2,remov:[2,3,6,8,9,13,54,71,72,77,92,108,116,118,142,146,147,148,149,150,151,155,156,157,158,160,161,168,171,172,197,206,210,215,228,239,240,245,251,253,255,261,262,263,274,275,276,278,284,290,299,300,302,314,317,318,319,321,337,355,365,390,417,422,469,472,480,481,495,496],remove_bia:8,remove_bias_al:8,remove_molecul:203,remove_sourc:203,remove_speci:203,ren:167,renam:[12,338,480],render:[12,13,191,193,194],rendon:[255,256],reneighbor:[3,8,12,39,57,71,210,214,231,314,327,337,391,486,487],renssela:284,renumb:71,reorder:[3,12,39,466],repeat:[2,6,193,194,210,217,218,231,307,358,377,453,455,457,464,483],repeatedli:2,repel:237,repes:191,replac:[2,3,6,11,12,41,63,89,90,119,145,146,147,148,149,150,151,154,155,156,157,158,160,161,191,193,194,195,206,207,209,210,211,212,214,217,221,239,260,287,294,296,387,409,470,471,476,477,487,495,496,497,499],replic:[],replica:[],replica_fil:12,report:[],repositori:[7,12,403,431,432,433],reprens:326,repres:[1,3,6,8,9,12,15,40,41,42,59,67,71,90,115,118,180,188,191,193,206,207,208,209,210,211,212,218,224,232,234,239,242,255,282,284,286,294,299,300,303,311,326,328,335,356,365,371,377,398,405,415,416,417,419,420,421,427,430,432,433,456,457,464,466,469,479,481,484,490,495,497],represent:[3,6,8,9,57,59,136,170,191,232,233,282,326,377,395,398,422,434,469,472,490],reprocess:474,reproduc:[3,255,332,387,393,399],repul:419,repuls:[6,7,9,36,40,45,46,110,237,290,331,332,335,372,376,377,385,387,391,395,399,401,415,419,423,440,449,455,458,461,462,479],reqir:[290,292],request:[3,6,8,12,41,104,171,188,191,236,242,297,314,316,353,355,424,432,433,464,474,479,483,495,496,497],requir:[],rerun:[],rescal:[],research:[5,7,242,246,422,464,483],resembl:294,reserv:[12,236,490],reservoir:[91,231,235,239,326],reset:[],reset_atomic_reference_posit:203,reset_dt:8,reset_target:8,reset_tim:203,reset_timestep:[],resid:13,residu:236,residue1:366,resist:[6,236],resolut:[208,440,452],resolv:[218,282,314,417],resort:3,resourc:[7,371,393],respa:[3,16,225,236,255,368,371,372,373,374,375,376,377,378,379,380,381,382,383,385,386,387,388,390,391,392,393,394,395,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,416,417,418,419,420,421,422,423,425,427,429,431,432,433,434,435,440,441,442,443,444,445,446,447,448,449,451,452,453,454,455,457,458,460,461,462,477,478,489,495],respecifi:422,respect:[1,6,9,10,13,14,15,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,42,43,45,46,47,48,49,51,53,54,56,59,70,71,87,89,97,98,111,114,120,124,145,150,153,155,162,166,167,174,175,177,178,179,180,182,183,185,186,188,193,194,210,211,216,217,218,220,234,237,239,240,242,255,257,258,259,260,261,262,263,264,265,272,274,275,276,278,290,291,299,300,303,311,313,326,331,334,340,342,343,345,346,349,351,353,355,356,360,363,364,369,370,371,372,374,376,377,378,379,380,381,382,38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Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso_e/atom command","compute meso_rho/atom command","compute meso_t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact_radius command","compute smd/damage command","compute smd/hourglass_error command","compute smd/internal_energy command","compute smd/plastic_strain command","compute smd/plastic_strain_rate command","compute smd/rho command","compute smd/tlsph_defgrad command","compute smd/tlsph_dt command","compute smd/tlsph_num_neighs command","compute smd/tlsph_shape command","compute smd/tlsph_strain command","compute smd/tlsph_strain_rate command","compute smd/tlsph_stress command","compute smd/triangle_mesh_vertices","compute smd/ulsph_num_neighs command","compute smd/ulsph_strain command","compute smd/ulsph_strain_rate command","compute smd/ulsph_stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style body/rounded/polygon command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":215,"default":[37,39,40,55,57,58,59,61,62,71,87,88,92,103,104,106,108,109,120,124,125,142,148,156,157,161,167,168,171,173,187,189,190,191,193,194,195,196,198,199,200,202,203,204,206,210,211,212,215,216,218,219,220,221,225,228,231,232,237,239,240,241,242,243,245,250,253,255,256,260,276,277,281,282,285,286,287,288,289,291,294,296,297,299,300,314,316,321,322,323,324,327,329,331,333,337,350,353,355,356,358,359,361,362,364,366,367,368,370,373,377,379,395,416,417,422,424,432,433,449,450,464,465,466,469,470,472,474,476,477,478,481,483,485,486,487,488,489,494,496,497,498],"function":495,"long":[208,378,380,381,382,383,387,389,390,407,411,415,427,435],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[198,199],addforc:200,addit:[12,13],addtorqu:201,adiabat:6,adjust_dt:304,adp:371,airebo:372,alloi:393,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:202,arrai:6,aspher:[6,82,146,257,261,265,266,274],atc:[9,203],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,92,96,97,100,101,102,108,112,113,115,142,143,166,202,204,205,288,495],atom_modifi:39,atom_styl:40,attract:5,aug:[],aveforc:213,awpmd:[9,373],balanc:[41,214],barostat:6,basal:67,beck:374,berendsen:[286,317],between:6,binary2txt:13,bodi:[6,8,42,68,147,258,262,267,275,375,376],bond:[8,13,69,215,216,217,295],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:377,born:[378,389],boundari:[7,57],box:[6,58,218],brownian:379,buck:[380,381,389,418],bug:3,build:[9,11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,174,382,415],chunk:[6,66,71,75,90,94,105,107,116,148,163,165,206],citat:7,class2:[21,43,175,340,383],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[331,385,461],colvar:[9,13,219],com:[74,75,149],comb3:386,comb:[291,386],come:5,comm_modifi:61,comm_styl:62,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,491,492,493,494,495,496,497,498,499],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,495],compute_modifi:103,condit:7,conduct:[6,322],constant:6,constraint:7,contact:76,contact_radiu:122,coord:77,core:6,correl:[207,208],cosin:[23,24,25,26,27,28,177],cossq:342,coul:[378,380,381,382,383,387,388,389,400,407,411,415,427,435],coupl:6,creat:216,create_atom:168,create_bond:169,create_box:170,createatom:13,creation:7,csld:318,csvr:318,cubic:409,cuda:[9,14,111,114,145,155,200,213,227,230,234,255,264,301,302,317,319,330,378,380,382,383,393,399,400,407,408,410,413,425,451,453],custom:8,cut:[49,373,380,383,387,390,395,397,407,408,415,423,427],cvff:343,damag:[78,123],data2xmovi:13,data:6,databas:13,deby:[387,407],dec:[],deform:[151,152,220],delete_atom:171,delete_bond:172,delta:24,deposit:221,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,491,492,493,494,495,496,497,498,499],diagnost:7,diel:388,dielectr:173,diffract:9,diffus:6,dihedr:[8,79],dihedral_coeff:176,dihedral_styl:[2,174,175,177,178,179,180,181,182,183,184,185,186,187,188],dilat:80,dimens:189,dipol:[6,29,390],direct:224,discuss:6,disp:6,displac:[81,86],displace_atom:190,distanc:344,distribut:[7,12],document:0,dpd:391,drag:222,dreid:[6,401],drude:[6,9,153,223,224,240],dsf:[387,407],dsmc:392,dump:[6,8,191,192,193,195],dump_modifi:194,dynam:290,eam:[13,393],echo:196,edip:394,eff:[9,13,97,98,152,154,159,241,256,268,277,320,395],efield:226,eim:396,elast:6,emac:13,enforce2d:227,ensembl:7,erot:[82,83,84,85],error:3,evapor:228,event:86,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,482,483,484,485,486,487,488,489,491,492,493,494,495,496,497,498,499],exp:[27,177],expand:[46,410],extend:[8,11],extern:229,fcc:280,featur:[7,8,495],fene:[45,46],fep:[9,13,87,199],field:[6,7],file:6,finit:6,fire:290,fix:[2,6,8,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,495],fix_modifi:[198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,218,219,220,221,222,224,225,226,227,228,229,230,231,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,283,284,285,286,287,288,289,290,291,292,293,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,328,329,330,331,332,333,334,335,336],flow:6,fluid:242,flux:[91,144],forc:[6,7,144,315],fourier:[30,31,178,345],freez:230,from:[6,11],futur:5,gauss:397,gaybern:398,gcmc:231,gener:[1,6,7,13],get:12,gld:232,gle:233,global:6,gpu:[9,15,374,378,380,382,383,385,387,390,391,393,397,398,400,407,408,409,410,423,425,434,435,442,451,452,453,460,461,462],gran:[332,399],granular:6,graviti:234,gromac:400,group2ndx:338,group:[88,337,495],gyrat:[89,90],h5md:[9,191,192],harmon:[32,47,48,49,179,182,331,346,426],hbond:401,heat:[91,144,235],heatconduct:443,helix:180,hertz:[399,436],hexord:92,histo:209,histori:[5,399],hook:399,hourglass_error:124,how:6,hybrid:[33,50,181,347,402],idealga:444,imag:[191,193],imd:236,implicit:382,improp:[8,93],improper_coeff:341,improper_styl:[2,340,342,343,344,345,346,347,348,349,350,351],includ:352,inclus:8,indent:237,indic:0,individu:2,induc:6,inertia:94,info:[0,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,218,219,220,221,222,224,225,226,227,228,229,230,231,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,283,284,285,286,287,288,289,290,291,292,293,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,328,329,330,331,332,333,334,335,336,353],input:[2,6,8],instal:11,instruct:9,integr:[6,7],integrate_tlsph:305,integrate_ulsph:306,intel:[9,16,255,264,265,380,382,398,407,451,453],interfac:[6,11],internal_energi:125,introduct:7,invers:224,ipi:238,ipp:13,jan:0,jul:[],jump:354,kate:13,keyword:424,kim:[9,403],kokko:[9,17],kspace:[2,8,9,327],kspace_modifi:355,kspace_styl:[6,356],label:357,lammp:[0,1,2,6,7,8,11,12],langevin:[239,240,241],lattic:358,lcbop:404,lennard:418,librari:[6,11,12],limit:[269,319],line:[12,270,405],linear:414,lineforc:247,list:[2,406],lj1043:331,lj126:331,lj93:331,lj96:408,lmp2arc:13,lmp2cfg:13,lmp2vmd:13,local:[6,65,68,69,79,93,110,117],log:359,lubric:416,lubricateu:417,make:12,mass:360,math:495,matlab:13,mdf:418,meam:[9,419,420,421],measur:1,meso:[248,249],meso_:100,meso_rho:101,meso_t:102,messag:3,mgpt:[9,422],micelle2d:13,mie:423,min_modifi:361,min_styl:362,minim:[8,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,218,219,220,221,222,224,225,226,227,228,229,230,231,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,283,284,285,286,287,288,289,290,291,292,293,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,328,329,330,331,332,333,334,335,336,363],misc:9,mod:[326,454],model:[6,7],modifi:8,molecul:364,molfil:[9,191,195],moltempl:13,momentum:[243,251],morri:448,mors:[51,401,425],move:252,move_tri_surf:307,movi:[191,193],mpi:11,msd:[104,105,106],msi2lmp:13,msm:[378,380,382,387,407],msst:253,multi:[6,7,182],multipl:6,nb3b:426,neb:[254,365],neigh_modifi:366,neighbor:367,nemd:6,newton:368,next:369,nharmon:183,noforc:[266,271],non:[6,7],none:[34,52,184,348,428],nongauss:106,nonlinear:53,nph:[255,256,257,258,259,299],nphug:260,npt:[255,256,261,262,263,299],nve:[264,265,266,267,268,269,270,271,272,273,299],nvt:[255,256,274,275,276,277,278,299],omega:107,omp:[9,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,43,45,46,47,48,49,51,53,54,56,174,175,177,178,179,180,182,183,185,186,188,234,255,257,259,260,261,263,264,272,274,276,278,291,340,342,343,345,346,349,351,371,372,374,378,379,380,381,382,383,385,386,387,388,390,391,393,396,397,398,399,400,401,402,405,407,408,409,410,411,412,413,414,415,416,420,421,425,426,427,429,434,435,442,451,452,453,454,455,457,458,460,461,462],onewai:279,open:7,oper:495,opl:185,opt:[19,382,393,407,411,425],optim:1,option:[6,8,12],orient:280,orientord:108,orthogon:6,other:6,output:[6,7,8,12,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,218,219,220,221,222,224,225,226,227,228,229,230,231,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,283,284,285,286,287,288,289,290,291,292,293,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,328,329,330,331,332,333,334,335,336],overlai:402,overview:11,packag:[1,9,12,14,15,16,17,18,19,370],pair:[6,109,110],pair_coeff:384,pair_modifi:424,pair_styl:[2,371,372,373,374,375,376,377,378,379,380,381,382,383,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,460,461,462],pair_writ:459,pairwis:8,parallel:11,paramet:6,pars:2,partial:155,particl:[6,7,42],partit:463,past:5,per:6,perform:[1,10],peri:429,period:25,phonon:[9,13,281],pimd:282,piston:333,planeforc:283,plastic:113,plastic_strain:126,plastic_strain_r:127,pmb:429,poem:[9,284],point:290,polariz:6,poli:[379,416,417],polygon:376,polym:13,polymorph:430,post:7,potenti:[2,6,8],pour:285,pppm:6,prd:464,pre:7,press:286,pressur:114,previou:12,print:[287,465],problem:[3,4],process:[6,7],processor:466,profil:156,properti:[6,115,116,117,288],pymol_aspher:13,python:[9,11,13,467],qbmsst:289,qeq:[290,291,292],qmmm:[9,293],qtb:[9,294],quadrat:186,quantiti:6,quartic:[35,54],quip:431,quit:468,ramp:157,rattl:302,rdf:118,read_data:469,read_dump:470,read_restart:471,reax:[9,13,292,295,296,432,433],reaxc:9,rebo:372,recent:297,reduc:119,refer:495,reflect:334,region:[8,119,158,159,335,472,495],relat:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,41,43,44,45,46,47,48,49,50,51,53,54,55,56,57,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,83,84,85,86,87,89,91,92,93,94,95,96,97,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,185,186,187,188,189,190,191,192,193,194,195,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,228,230,231,232,233,234,235,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,283,284,285,286,287,288,289,290,291,292,294,295,296,297,299,300,301,303,304,305,306,307,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,349,350,351,352,353,354,355,356,358,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,429,430,431,432,433,434,435,436,437,438,439,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,474,475,476,477,478,479,481,482,483,484,485,486,487,488,489,491,492,493,495,496,497,498,499],relax:218,replic:473,replica:[6,7],report:3,requir:12,rerun:474,rescal:[319,320],reset:225,reset_timestep:475,resquar:434,restart2data:13,restart:[6,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,218,219,220,221,222,224,225,226,227,228,229,230,231,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,283,284,285,286,287,288,289,290,291,292,293,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,328,329,330,331,332,333,334,335,336,476],restrain:298,restrict:[14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,491,492,493,494,495,496,497,498,499],rho:128,rhosum:446,rigid:[6,83,99,245,299],ring:349,rotat:160,round:376,rule:2,run:[6,11,12,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,218,219,220,221,222,224,225,226,227,228,229,230,231,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,283,284,285,286,287,288,289,290,291,292,293,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,328,329,330,331,332,333,334,335,336,477],run_styl:478,scalabl:10,scalar:6,screen:12,script:[2,6,8,11],sdk:[36,435],self:313,serial:11,set:[6,479],setforc:301,setvel:308,shake:302,share:[11,12],shell:[6,480],shield:290,shift:[26,27,48,49,177],simpl:31,simul:6,size:6,slater:290,slice:121,sllod:[276,277],small:299,smd:[9,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,303,304,305,306,307,308,310,436,437,438,439],smooth:[413,414],smtbq:[9,440],sna:142,snad:142,snap:441,snapshot:6,snav:142,soft:[415,442],solver:2,sourc:7,spatial:[210,211],spc:6,speci:296,special:[7,424,495],special_bond:481,sph:[9,443,444,445,446,447,448],sphere:[84,85,161,211,245,259,263,272,278],spheric:6,spline:[420,421],spring:[311,312,313,324],squar:28,srd:[314,336],srp:449,standard:9,start:[12,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,218,219,220,221,222,224,225,226,227,228,229,230,231,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,283,284,285,286,287,288,289,290,291,292,293,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,328,329,330,331,332,333,334,335,336],state:316,stationari:249,stop:[198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,218,219,220,221,222,224,225,226,227,228,229,230,231,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,283,284,285,286,287,288,289,290,291,292,293,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,328,329,330,331,332,333,334,335,336],store:[315,316],strategi:1,streitz:387,stress:[143,144],structur:2,style:[1,2,6,8],submit:8,suffix:482,summari:6,swap:[204,217],syntax:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,281,282,283,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,491,492,493,494,495,496,497,498,499],system:6,tabl:[0,6,38,56,188,452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\ No newline at end of file
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6,336,349,355,361,362,363,365,366,367,370,395,416,417,424,466,467,469,471,472,474,477,479],affin:[16,17,18,220,370,386],afil:233,aforement:18,afresh:[287,477,495],afshar:391,after:[2,3,5,6,8,9,11,12,15,21,22,33,39,40,41,44,50,57,58,59,61,63,71,146,147,148,149,150,151,152,155,156,157,158,160,161,168,169,171,172,175,176,181,190,191,192,193,194,195,197,198,199,203,204,206,207,214,215,216,217,218,220,224,231,242,243,244,245,246,251,252,253,255,261,262,263,269,274,275,276,278,281,285,289,297,299,302,310,315,317,318,319,321,322,323,324,325,329,331,333,337,340,341,347,354,360,361,363,364,366,368,369,370,371,372,377,384,386,393,394,395,396,402,403,404,415,416,417,419,420,421,422,426,430,432,433,440,441,451,453,454,455,458,464,466,468,469,470,471,472,474,475,477,479,481,483,486,487,490,494,495,496,497,498,499],afterrun:477,afterward:3,afterword:41,ag1:167,ag2:167,again:[6,11,12,16,17,62,142,148,154,162,191,194,220,235,285,340,354,365,416,417,464,466,467,469,471,476,483,485,495,497],against:[11,12,13,64,221,365,432,433],aggreg:[6,12,65,68,69,79,93,110,117,235,251,297,299,312,464,496],aggress:[235,483],agilio:[9,13],agre:[3,8,188,363,372,404,433],agreement:[5,7],ahd:401,ahead:333,aidan:[0,5,7,9,13,358],aij:13,aim:6,airebo:[],ajaramil:[7,9,13],aka:193,akohlmei:[7,9,13,195,236],aktulga:[7,9,292,433],al2o3:440,al2o3_001:[120,300],al3:167,ala:[242,440],alain:9,alat:[280,419],alb:[430,453,455],albeit:298,albert:9,alchem:[87,162],alcohol:329,alcu:[371,377],alcu_eam:430,alderton:390,alejandr:[255,256],alessandro:13,algebra:422,algorithm:[0,1,6,7,8,9,41,61,194,203,214,217,220,242,244,245,269,282,290,299,302,321,322,326,329,334,361,362,363,367,370,395,417,422,437,439,464,466,483],alia:[12,16],alias:[1,356],aliceblu:194,align:[6,12,29,41,71,170,188,210,214,237,358,469,472,490],alkali:395,all:[0,1,2,3,5,6,7,8,9,11,12,13,14,15,16,17,18,22,33,37,39,40,41,42,44,50,54,55,57,59,60,61,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,156,161,162,163,164,165,166,167,168,169,170,171,172,174,176,181,187,188,191,192,193,194,195,197,198,199,200,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,223,224,225,226,227,228,229,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,248,250,251,253,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,272,273,274,275,276,277,278,279,280,281,282,284,285,286,287,288,289,290,291,292,294,295,296,297,298,299,300,301,302,303,304,305,306,310,311,313,314,315,316,317,318,321,322,323,324,325,326,327,328,329,331,332,333,334,335,336,337,338,339,340,341,345,350,353,354,355,356,357,358,360,363,364,365,366,367,369,370,371,372,373,375,376,377,378,380,381,382,383,384,386,387,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,411,415,416,417,418,419,420,421,422,423,424,425,426,427,429,430,431,432,433,434,435,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,461,462,463,464,466,467,468,469,470,471,472,473,474,476,477,478,479,480,481,482,483,484,486,487,488,490,494,495,496,497,498,499],allen:[29,87,390,398],allentildeslei:87,allign:3,allindex:338,alloc:[3,5,6,8,9,11,12,60,229,328,364,366,370,428,433,469,477],allocat:3,alloi:[],allosw:71,allow:[1,2,3,6,8,9,11,12,13,14,15,16,17,18,22,37,39,40,41,55,57,58,59,61,62,63,77,92,108,110,144,146,147,148,161,166,167,168,170,176,187,188,191,193,194,195,197,198,200,202,203,204,206,207,208,209,210,211,212,214,216,217,218,219,220,221,225,226,229,231,232,233,234,236,239,242,245,246,250,252,255,256,280,284,286,287,288,289,293,299,300,302,303,305,306,310,314,321,322,323,324,326,327,328,329,330,331,337,339,341,350,355,356,358,363,364,365,366,369,370,373,377,378,379,380,381,382,387,393,395,399,400,401,402,407,411,416,417,422,424,430,433,434,437,439,440,449,459,461,464,467,469,471,472,473,474,475,476,479,481,482,483,486,487,495,496],almost:[2,3,12,60,237,289,326,356,367,370,449],alo:387,alon:[6,7,217,295,432,433,467],alond:13,along:[6,8,9,12,29,40,71,87,120,167,168,190,191,193,206,217,237,242,243,247,252,254,289,299,302,303,307,311,312,321,325,326,332,335,337,358,361,362,363,365,387,390,399,402,405,407,411,419,432,433,452,469,472,479,480,495],alonso:[420,421],alpha:[6,12,51,198,242,281,289,290,294,363,371,374,378,387,391,393,394,396,401,406,407,419,425,429,454,456,487,490],alpha_:[],alpha_c:415,alpha_i:441,alpha_ialpha_j:[],alpha_lj:415,alphabet:[2,3,22,37,44,55,63,176,187,197,341,350,364,384,450,469],alphanumer:[3,63,197,288,296,339,364,495],alreadi:[3,7,8,9,12,16,17,18,42,168,169,171,192,202,206,210,211,214,216,220,246,287,289,314,337,364,365,391,400,402,409,417,449,459,462,465,469,470,474,479,495],also:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,22,29,36,37,38,39,40,41,42,44,54,55,56,58,59,61,63,66,71,7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6,398,496],chiefli:431,child:8,chip:[7,12,17,18,370,482],chipot:219,chiral:349,chmod:[11,12],cho:419,chocol:[7,194],choic:[3,6,12,15,16,18,40,41,54,87,143,146,147,161,172,188,206,210,211,214,217,220,221,233,239,242,253,255,282,290,299,321,350,356,361,362,365,367,370,402,415,424,428,469,478,479,482,483,489,490,494],choos:[1,3,6,7,8,12,16,17,18,29,39,54,87,119,158,159,193,215,216,217,218,221,228,239,242,253,255,257,258,259,260,261,262,263,286,314,318,332,355,356,362,459,464,466,478,484],chose:[453,455],chosen:[2,3,6,12,17,142,168,171,180,188,193,199,204,218,221,228,231,232,240,242,253,255,260,282,285,296,314,318,321,322,327,329,330,336,356,357,362,370,395,399,406,409,435,453,464,478,483,490],chri:166,christian:[7,9,14,17],christoph:7,chunk:[],chunkid:[66,75,90,94,105,107,116,148,163,165,206],chute:[4,10,234],ciccotti:302,cieplak:[6,174,481],cii:207,cij:207,circl:[42,71,310],circular:[3,6,146,189],circumst:18,circumv:[92,108,294],citat:[],cite:[3,7,8,12,239,440],ckio:2,cko:2,cl1:167,clarendon:[29,390],clarifi:[7,453,455],clariti:339,clark:427,class2:[],classic:[0,3,5,6,7,8,9,229,282,289,294,326,351,395],classifi:[9,450,458],claus:467,clean:[6,12,14,15,17,477],cleanli:[468,498],clear:[],clearli:7,clebsch:142,clermont:[9,13],clever:473,click:[2,11,22,37,44,55,168,176,187,193,236,341,350,365,384,450],client:[236,238],climb:[254,365,483],clinic:[7,13],clo:[157,190,496],clock:[12,464,483],clockwis:332,close:[3,6,11,12,13,39,41,67,71,143,171,191,216,217,218,233,240,242,255,276,299,302,332,335,354,356,359,361,362,365,370,372,377,387,388,405,419,424,436,438,455,473,479,490,492],closer:[3,41,118,166,190,191,214,218,222,323,365],closest:[216,280,299,329,398,434,449,459],cloud:[440,490],clovertown:18,clsuter:72,clump1:[284,299],clump2:[284,299],clump3:[284,299],clump:299,cluster:[],clutter:[3,9],cmap:469,cmatrix:233,cmax:419,cmd:[11,12,282,480],cmdarg:11,cmin:419,cmm:[],cn1:207,cn2:207,cna:[],cnn:207,cnr:[9,13],cnt:[402,473],co2:[40,167,302,364],coars:[7,9,29,36,40,54,180,284,299,314,400,435,481],coarser:[356,495],coarsest:142,code:[],coeff:[3,7,8,12,21,22,33,44,50,174,175,176,181,340,341,347,384,402,406,424,437,439,442,469],coeffcient:469,coeffici:[],coefficienct:391,coefficient0:393,coefficient1:393,coeffieci:[6,374,405],coeffincientn:393,coexist:[9,231,395],cohes:[6,396,419],coincid:[124,335,382,416,417,464],colberg:192,cold:[6,153,231,235,366,490],coldest:322,coleman8:9,coleman:[9,120,167,300],colin:9,collabor:[7,8,9,15],collect:[3,6,7,8,9,13,40,42,66,75,83,90,94,99,105,107,116,148,156,163,165,168,191,194,206,219,245,251,284,294,297,299,337,355,364,366,385,469,476,482,488,499],collid:[225,314,336],colliex:167,collinear:[3,284],collis:[3,242,314,332,336,392,399,462],colllis:314,colloid:[],colombo:39,colon:[195,337,470],color1:194,color2:194,color:[3,9,41,191,193,194,214,232,289,294],column:[3,6,9,12,13,42,63,65,66,67,68,69,71,75,77,79,81,90,92,93,94,105,107,108,110,112,115,116,117,118,119,121,142,143,148,156,163,165,166,167,188,191,194,197,205,206,207,209,210,211,212,245,252,253,289,299,315,316,326,336,397,401,432,433,470,484,486,495],colvar:[],colvarmodul:12,com:[],comamnd:220,comand:217,comannd:370,comb3:[],comb:[],comb_1:291,comb_2:291,combiant:388,combin:[3,6,7,9,11,13,36,40,63,65,69,79,87,93,104,110,117,146,147,161,191,193,203,209,236,245,255,282,288,318,327,335,338,340,355,356,358,362,370,385,387,388,395,396,402,414,415,441,451,453,455,458,461,472,477,482,490,495],come:[],comfort:[12,13],comm:[0,3,11,12,61,73,192,236,238,239,356,365,370,391,424,429,452,471],comm_modifi:[],comm_modift:61,comm_styl:[],comm_world:11,command:[],comment:[2,7,11,12,38,56,174,188,191,240,299,326,364,365,371,393,394,396,406,419,426,433,440,441,451,452,453,454,455,458,466,467,469,490,495],commerci:7,commmand:[3,6,12,59,109,277,405,463,464,466,483,498],common:[],commonli:[3,6,12,17,25,57,59,106,108,170,191,193,195,351,400,409,441,453,455,469,472,481],commun:[1,3,6,7,8,10,11,12,14,15,16,18,40,41,58,61,62,71,171,172,193,194,214,215,216,218,219,220,236,238,242,244,245,246,255,281,288,290,291,292,299,314,326,337,353,355,366,367,368,370,392,428,466,467,478,479,495,497,499],communc:355,comp:[7,192,238,239,302,356,365,395,424,429,434,448,452,454],compact:[63,197,384,450],compani:[5,7],compar:[1,3,4,6,8,12,17,39,86,112,120,151,166,167,176,187,194,224,290,337,339,355,356,363,365,419,440,464,483,484,490,494],comparison:[],comparison_of_nvidia_graphics_processing_unit:14,compass:[7,21,22,37,43,44,55,175,176,187,340,341,350,383,450],compat:[3,5,7,8,9,11,12,13,17,18,41,71,119,121,179,191,195,199,205,206,207,209,210,211,212,214,281,293,318,321,328,331,334,355,370,403,422,424,452,466,467,495],compens:[6,215,216,297,366,395],compet:325,competit:356,compil:[3,7,8,9,10,12,13,14,15,16,17,18,19,166,191,192,193,195,236,325,356,370,422,469,470,474,495],compl:17,complain:[12,17],complement:419,complementari:[7,387,407],complet:[3,6,9,11,12,15,41,59,71,194,210,214,219,245,282,285,288,314,325,327,339,354,365,370,396,437,439,457,464,469,474,477,481,483,486,490,495],complex:[6,8,11,12,13,25,40,42,62,92,108,142,144,156,168,169,242,310,335,353,365,395,422,452,467,469,472,495],compli:[321,325],complic:[6,7,9,12,13,204,231,467],complier:12,compon:[3,6,8,12,61,63,66,67,73,81,88,89,90,91,92,94,95,98,105,106,107,108,109,110,111,112,114,115,119,129,132,133,134,135,138,139,140,142,143,145,146,147,148,149,150,151,152,153,154,155,156,157,158,160,161,163,164,165,190,191,193,194,200,201,205,206,207,208,209,210,211,212,213,217,218,220,221,226,229,234,238,239,242,245,247,251,252,254,255,256,260,261,262,263,274,275,276,278,279,281,282,283,286,297,299,301,302,303,307,308,311,314,317,318,319,321,328,329,334,335,336,355,358,362,363,364,365,370,376,391,395,399,416,417,437,439,440,441,469,470,479,487,495,496],componenet:6,composit:[6,204,242,393],compound:[386,395,396,458],compres:[71,116,206],compress:[],compris:[40,335,434,457],compton:[120,167],comptu:3,compuat:356,comput:[],computation:[3,6,215,216,326,377],computational:490,compute_arrai:8,compute_fep:[199,415],compute_group_group:231,compute_inn:8,compute_ke_atom:8,compute_loc:8,compute_modifi:[],compute_peratom:8,compute_sa:[120,300],compute_scalar:8,compute_temp:8,compute_ti:199,compute_vector:8,compute_xrd:167,concaten:[2,3,498],concav:335,concentr:[71,393],concept:[6,148,158,206,478],conceptu:[3,6,71,156,218,220,365,387,402,419,474],concern:[6,73,87,192,232],concetr:71,concis:[11,325],conclud:12,concret:8,concurr:[9,16,356,495],conden:[326,453,455],condens:[6,150,326,372,389,393,407,458],condit:[],conducit:6,conduct:[],cone:472,confer:422,confid:[3,483],config:[12,191,466],configfil:219,configur:[1,2,6,12,15,17,38,59,124,170,188,190,191,193,197,218,219,220,221,225,231,238,239,269,282,290,325,353,363,365,372,377,394,419,422,451,453,455,458,464,469,471,472,483],confin:[469,483],conflict:[3,12,40,424,467],conform:[3,6,13,59,217,218,254,298,303,325,349,365,395,481],confus:[3,458],conjuct:391,conjug:[7,8,239,362,395,432,433],conjunct:[6,7,71,86,87,116,151,156,162,168,172,194,198,199,239,242,246,269,285,286,290,291,292,294,299,314,322,329,334,355,356,365,378,380,384,387,391,395,401,407,424,427,435,456,469,472,476,490,499],connect:[3,6,87,153,171,217,236,284,299,302,311,365,388,399,449,455,466,467,473,490],conput:3,consecut:[3,11,12,39,71,168,194,198,199,221,236,237,387,407,411,464,470,472],consequ:[1,6,204,326,406,483],conserv:[3,29,197,204,217,224,225,232,235,239,241,242,246,251,253,255,269,299,302,317,318,322,329,330,334,365,390,391,399,413,440,478,483],consid:[6,9,70,71,78,87,117,150,153,154,171,191,194,198,199,205,207,210,214,216,217,221,243,256,281,299,321,322,325,326,329,356,384,395,402,433,434,440,449,464,465,467,470,471,472,474,477,479,487,490,495],consider:[6,8,239,240,317,318,319,370,478],consist:[3,6,8,9,11,12,40,42,65,69,79,93,105,110,113,114,117,148,151,153,168,180,190,195,200,201,206,220,221,224,226,229,232,239,240,241,252,255,257,258,259,260,261,262,263,264,265,267,268,269,270,272,273,274,275,276,277,278,286,289,294,296,298,299,317,318,319,320,330,355,356,358,364,365,370,372,377,379,385,387,395,398,402,405,416,417,419,422,424,434,437,439,440,452,459,467,469,470,471,472,473,474,481,490,495],consistent_fe_initi:203,consit:299,constant:[],constitu:[3,6,245,299,331,335,385,434],constitut:[437,439],constrain:[3,6,8,145,146,147,148,149,151,154,155,156,157,158,160,161,197,206,221,231,232,237,245,249,284,285,297,299,302,312,322,329,363,364,395,474,481,490],constraint:[],construct:[6,8,12,14,38,54,56,61,64,67,70,72,73,77,92,108,120,142,167,218,255,281,298,335,366,370,390,422,424,449,451,452,472,473,488,495],constructor:[8,11],consult:433,consum:[1,294,428,495],consumpt:353,contact:[],contact_stiff:[436,438],contain:[0,1,2,3,4,6,8,9,11,12,13,17,18,19,38,40,41,56,63,87,91,118,120,142,148,156,166,167,168,170,174,176,187,188,191,193,194,195,197,198,199,203,205,206,207,209,210,211,212,214,219,221,226,233,237,238,239,242,253,269,280,281,284,285,287,289,292,296,299,300,304,314,321,325,326,335,336,339,354,356,364,365,368,369,371,372,373,377,386,387,390,393,394,395,402,403,419,422,426,430,431,432,433,441,451,452,453,454,455,456,458,464,465,466,467,469,470,471,472,474,476,478,481,483,486,487,490,495,497,499],content:[12,18,433,485,487],context:[3,6,8,12,17,118,119,194,215,216,221,284,296,330,362,461,469,476,485,494,495,496],contibut:70,contigu:466,contin:16,continu:[0,2,3,5,6,9,12,13,14,41,71,81,104,105,164,194,197,198,199,204,206,207,208,209,210,211,212,214,217,218,219,220,221,231,232,233,235,236,237,239,240,241,247,252,253,255,257,258,259,260,261,262,263,274,275,276,277,278,283,285,288,289,299,300,303,313,314,316,323,324,326,332,335,339,354,369,370,377,391,392,409,412,432,433,434,437,439,454,464,467,469,471,472,477,483,486,487,495,497],continuum:[6,7,9,203,326,437,439],contour_integr:203,contract:[59,218,220,255,286,299],contradictori:3,contrain:302,contraint:269,contrari:[233,240],contrast:[1,6,42,55,64,150,153,220,337,437,439,461,498],contrib:326,contribut:[3,5,6,7,8,9,12,13,17,63,66,68,70,71,74,75,77,80,84,87,88,89,90,91,94,103,105,107,109,110,111,112,114,116,119,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,199,204,205,206,207,209,210,211,212,218,231,239,242,245,246,250,256,276,277,284,285,293,296,299,300,302,328,355,363,365,373,391,392,393,395,402,416,417,422,424,432,433,440,481,487,490],contributor:12,control:[3,5,6,7,8,9,11,13,16,27,29,41,87,91,124,142,177,191,193,197,203,204,214,218,219,220,235,236,239,240,255,257,258,259,260,261,262,263,286,291,299,305,306,317,318,319,326,330,353,355,367,395,398,422,432,433,436,438,451,455,464,466,478,484,485],control_typ:203,controlfil:433,convect:91,conveni:[6,12,29,191,195,212,300,358,441,495],convent:[3,8,9,29,179,186,187,194,298,311,338,393,395,495],converg:[3,6,41,88,191,193,195,200,214,217,218,226,229,260,289,291,294,298,302,361,362,363,365,386,387,407,440,464,476,483],convers:[3,8,142,193,194,204,207,286,355,387,388,389,395,407,411,415,427,467,483,494],convert:[2,3,4,5,6,7,8,12,13,20,21,24,28,32,35,36,59,63,71,91,168,175,191,193,194,212,253,337,340,342,346,349,358,365,371,393,422,453,455,462,467,469,470,471,476,486,490,494,495,497,499],convex:[42,335,376],convinc:[7,12],cook:9,cooki:7,cool:[7,158,235,297],cooordin:191,cooper:[5,7],coord123:116,coord1:[3,116,206,210,211],coord2:[3,116,206,210,211],coord3:[3,116,206,210,211],coord:[],coordb:440,coordbb:440,coordiat:363,coordin:[1,3,4,6,7,8,11,13,14,15,17,40,41,42,59,61,62,63,66,68,71,74,75,77,81,87,89,90,94,104,105,107,115,116,118,136,142,151,157,163,165,166,168,172,190,191,192,193,194,195,197,200,205,206,209,210,211,214,215,216,217,218,219,220,221,224,226,227,229,231,234,235,236,237,238,239,240,252,254,255,257,258,259,261,262,263,276,279,280,281,284,285,286,296,297,299,301,302,303,308,311,312,313,314,316,324,325,326,333,334,336,337,358,363,364,365,370,371,372,375,376,394,440,464,469,470,471,472,474,477,479,483,490,495,496],coordn:[116,206],coorind:[],copi:[0,3,4,8,11,12,15,17,40,121,193,326,365,384,432,467],copper:462,coproccesor:16,coprocessor:[1,4,7,9,16,17,370,482],coproprocessor:17,copy_arrai:8,copyright:[7,8,284],coral:194,core:[],core_shel:150,coreshel:[6,9,380,387,389],cornel:[6,174,481],corner123i:115,corner123x:115,corner123z:115,corner1i:115,corner1x:115,corner1z:115,corner2i:115,corner2x:115,corner2z:115,corner3i:115,corner3x:115,corner3z:115,corner:[3,6,40,115,193,335,336,358,457,469],cornflowerblu:194,cornsilk:194,corpor:16,corr:386,correct:[3,6,9,11,12,16,17,59,87,88,103,104,112,118,150,155,162,193,220,231,233,239,255,256,276,284,286,289,325,331,335,355,365,371,372,373,374,375,376,377,378,379,380,381,382,383,385,386,387,388,389,390,391,392,393,394,395,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,427,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,457,458,460,461,462,469,484,487,490],correction_max_iter:203,correctli:[3,8,9,11,17,71,81,103,104,105,145,146,147,149,151,153,154,155,156,157,160,161,164,191,194,200,221,226,229,240,249,255,256,292,299,302,311,313,332,335,365,366,370,389,417,422,466,467,469,479,494,496],correl:[],correspond:[1,2,6,8,11,12,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,40,42,43,44,45,46,47,48,49,51,53,54,56,70,71,87,97,98,111,114,115,116,117,120,121,129,132,133,134,135,136,138,139,140,142,145,146,155,162,167,174,175,176,177,178,179,180,182,183,185,186,188,190,191,193,194,198,199,200,206,208,209,210,211,213,216,218,220,227,229,230,234,239,242,243,251,252,253,255,257,258,259,260,261,262,263,264,265,269,272,274,275,276,278,281,282,286,291,299,301,302,317,319,321,330,331,332,334,335,336,338,340,341,342,343,345,346,349,351,356,360,362,364,365,371,372,374,378,379,380,381,382,383,384,385,386,387,390,391,393,394,395,396,397,398,399,400,401,402,405,407,408,409,410,411,412,413,414,415,416,419,420,422,424,425,426,427,429,430,432,433,434,435,440,441,442,451,452,453,454,455,457,458,460,461,462,464,466,467,469,470,472,482,483,484,486,487,490,495],correspondingli:[416,417,478],cosin:[],cosineshift:27,cosmo:[233,238],cossq:[],cost:[1,6,10,11,12,17,39,41,71,111,120,143,167,193,194,206,210,211,214,215,216,228,255,291,326,355,356,368,387,407,411,422,424,451,466,478],costheta0:[451,453,455,458],costheta:430,costli:[11,88,233,366],couett:4,coul:[],could:[2,3,6,9,11,12,17,33,41,50,59,66,71,75,87,90,94,105,107,111,114,116,148,158,163,165,181,191,193,194,198,199,206,207,210,214,220,229,238,288,289,290,294,297,299,301,314,315,321,325,326,327,331,335,337,339,347,352,354,361,363,366,370,373,397,401,402,405,432,433,465,466,467,469,471,473,476,477,485,490,495,496],coulomb:[3,5,6,7,8,9,10,12,14,15,18,72,88,109,110,118,143,169,173,290,292,327,355,356,363,370,378,380,381,382,383,386,387,388,389,390,395,399,400,402,407,411,415,418,424,427,432,433,435,440,450,455,456,458,461,474,481,487,490,494],coulommb:6,cound:3,count:[1,3,6,8,10,11,12,16,41,63,68,77,91,116,118,119,156,166,172,200,201,204,206,209,210,211,213,214,221,226,228,231,237,255,269,285,302,317,318,335,356,363,364,365,367,370,397,401,424,487,495],counter:[332,464,475,477,483],counteract:231,counterbal:235,counterbalanc:29,counterpart:[191,299,464],counterproduct:18,coupl:[],courant:304,cours:[3,8,128,130,162,191,198,199,232,298,311,325,331,333,334,336,337,356,416,442,466,469,482,490,495,497],courtesi:358,cov:440,coval:[6,29,395,419,440,490],covari:233,cover:[6,71,188,194,203,242,395,457],coverag:[71,210],cpc:238,cpp:[1,3,6,8,9,11,12,13,87,191,198,199,229,302],cpu:[1,3,4,9,10,12,14,15,16,17,18,63,71,194,208,224,240,327,353,356,370,384,450,464,482,483,486,487,488,495],cpuremain:487,cr2:167,cr3:167,crack:[4,366],crada:[5,7],crai:[5,7,13,18,191],crash:[3,12,366,490],craympi:370,creat:[],create_atom:[],create_bond:[],create_box:[],create_elementset:203,create_faceset:203,create_group:192,create_nodeset:203,createatom:[],creation:[],crimson:194,critchlei:284,criteria:[3,118,169,193,194,215,216,217,250,363,429,457,471,474,495],criterion:[12,41,123,166,168,171,204,214,217,231,269,291,304,332,337,363,365,386,395,399,440,474,483,484],criterioni:483,critic:[6,48,49,253,321,326,363],crmax:71,crmin:71,cross:[3,12,22,71,89,146,176,191,193,205,210,216,220,252,254,276,299,307,311,313,322,329,341,358,365,382,391,392,393,400,401,402,407,409,411,430,435,437,439,453,455,462,469,473,479,497],crossov:1,crossterm:469,crozier:[0,7,13],crucial:289,crystal:[4,6,13,73,108,280,281,324,358,366,473,487,490],crystallin:[6,104,281,358,454,490],crystallis:321,crystallogr:[120,167],crystallograph:[358,487],crystallographi:[120,167,358],cs1:167,cs_chunk:6,cs_im:[40,469],cs_re:[40,469],csanyi:[142,431,441],cscl:419,csequ:6,csh:[11,12,384],cshrc:[11,12],csic:[394,451,453,455,458],csinfo:6,csisi:[394,451,453,455,458],csld:[],cst:393,cstherm:6,cstyle:466,csvr:[],ctcm:[371,393],ctemp_cor:224,cterm:303,ctr:9,ctype:11,cu1:167,cu2:167,cu3au:419,cube:[6,41,166,171,214,224,335,358,490],cubic:[],cuda:[],cuda_arch:15,cuda_get:15,cuda_hom:15,cuda_prec:15,cufft:14,cuh:377,cummul:[3,6,212,215,216,217,219,228,233,239,241,314,317,318,319,320,322,329,401,487],cumul:[6,204,206,209,210,211,225,231,239,253,255,260,269,299,300,365],curli:2,current:[0,1,3,5,6,7,8,9,11,12,13,15,16,17,18,40,41,42,59,61,63,71,73,81,87,103,104,110,118,119,132,143,148,156,158,164,166,169,172,190,191,192,193,194,195,198,199,203,206,210,211,212,214,215,216,217,218,219,220,221,225,226,229,231,233,236,237,239,245,252,255,256,261,262,263,269,274,275,276,278,284,290,291,293,296,297,298,299,302,303,304,305,306,307,308,310,312,313,314,317,318,319,325,326,329,330,331,332,333,334,336,337,339,353,354,355,356,359,360,362,363,364,365,370,376,377,384,386,390,393,395,396,399,402,403,406,416,417,419,420,421,424,430,432,433,436,437,438,439,442,453,455,456,459,464,465,466,467,469,470,471,472,473,475,476,477,479,481,483,484,486,487,495,496,497,498,499],curv:[6,168,231,281],curvatur:[398,434,462],custom:[],cut0:467,cut1:478,cut2:478,cut:[],cuthi:[280,292],cutinn:[379,416,417],cutlo:[280,292],cutmax:430,cutoff1:[383,390,407,411,415,418,427,435],cutoff2:[378,380,381,383,389,390,407,411,415,418,427,435],cutoff:[3,6,10,16,18,39,45,46,54,55,61,70,72,73,77,87,92,108,110,117,118,142,166,169,171,216,217,222,280,289,290,292,294,296,299,314,327,331,335,337,353,355,356,363,366,367,368,370,371,372,373,374,375,376,377,378,379,380,381,382,383,385,387,388,389,390,391,392,393,394,395,396,397,398,400,401,402,403,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,432,433,434,435,440,441,442,443,444,445,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,467,471,474,478,490,495],cutoff_glob:376,cutoff_inn:376,cutoffa:394,cutoffc:394,cuu3:393,cval:167,cvd:321,cvel:303,cvff:[],cwiggl:[3,252,331,334,336,495],cyan:[2,193,194],cycl:[3,231,253,255,256,260],cyclic:[3,188],cygwin:12,cylind:[3,4,71,193,206,237,285,332,335,472],cylindr:[6,237,311,332],cypress:370,cyrot:377,cyrstal:281,d3q15:242,d3q19:242,d_double_doubl:15,d_e:326,d_flag2:288,d_flag:288,d_name:[115,191,288,316,479],d_single_doubl:15,d_single_singl:15,d_sx:288,d_sy:288,d_sz:288,daan:324,dai:12,daili:12,daivi:276,damag:[],dammak:294,damp:[3,6,197,202,239,240,241,246,255,256,260,286,289,290,294,299,317,318,330,332,333,362,363,365,378,380,382,387,390,395,399,407,415,427,435,450,456,483,490],damp_com:240,damp_drud:240,dampen:[299,490],dampflag:[332,399],dan:17,danger:[3,12,231,337,391,487],dangl:171,daniel:9,darden:[356,390],darkblu:194,darkcyan:194,darken:193,darkgoldenrod:194,darkgrai:194,darkgreen:194,darkkhaki:194,darkmagenta:194,darkolivegreen:194,darkorang:194,darkorchid:194,darkr:194,darksalmon:194,darkseagreen:194,darkslateblu:194,darkslategrai:194,darkturquois:194,darkviolet:194,dasgupta:290,dash:[399,486],dat:[6,91,188,203,465],data2xmovi:[],data:[],data_atom:8,data_atom_hybrid:8,data_bodi:8,data_vel:8,data_vel_hybrid:8,databas:[],datafil:[12,13,300],dataset:300,datatyp:3,date:[0,6,12,13,190,432,433,495],datom1:117,datom2:117,datom3:117,datom4:117,datum:[3,6,42,65,68,69,79,93,110,117,191,207],davenport:418,davi:331,david:[9,19,355,356,453,455],daw:[393,430],dbg:14,dcd:[3,6,7,191,192,193,194,195,282,470,474],ddim:190,deactiv:415,dealt:238,debug:[6,7,11,12,13,14,17,120,124,167,168,282,287,353,355,370,403,424,459,467,468,476,479,486,495],deby:[],decai:[92,387,462],decid:[3,6,12,16,71,252,288,299,327,484],decipher:358,declar:192,declin:314,decod:193,decompos:[87,441],decomposit:[3,5,7,18,62,203,282],decoupl:[6,490],decreas:[3,191,200,201,208,217,220,226,229,231,239,325,355],decrement:303,deepli:352,deeppink:194,deepskyblu:194,def:[12,13,467],defaul:61,defect:[6,70,166,422],defgrad:2,defin:[2,3,5,6,7,8,11,12,17,20,21,22,23,24,25,26,27,28,29,30,31,32,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,51,53,54,55,56,57,58,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,174,175,176,177,178,179,180,182,183,185,186,187,188,189,190,191,192,193,194,197,198,199,200,201,202,203,204,205,206,207,209,210,211,212,213,214,215,216,217,218,220,221,224,225,226,229,230,231,234,237,238,239,240,241,242,250,252,254,255,256,257,258,259,260,261,262,263,265,266,267,270,272,273,274,275,276,277,278,280,281,282,284,285,286,288,290,292,297,299,300,301,302,304,308,312,314,316,317,318,319,320,322,323,324,326,328,329,331,332,333,334,335,336,337,339,340,341,342,343,344,345,346,349,350,351,353,355,356,358,360,362,363,364,365,366,367,368,369,370,372,373,374,375,376,378,379,380,381,382,383,384,385,387,388,390,391,392,394,395,397,398,399,400,401,402,403,405,407,408,409,410,411,412,413,414,415,416,417,418,422,423,424,425,426,427,429,430,432,433,434,435,436,437,438,439,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,466,467,469,470,472,473,474,475,478,479,480,481,483,484,486,487,490,491,492,493,494,495,496],definit:[2,3,6,8,12,13,78,80,118,142,194,206,207,208,209,210,211,212,220,237,260,300,316,328,331,334,336,338,350,353,364,373,377,385,395,405,430,437,439,441,457,467,469,471,478,480,494,495],defint:487,deform:[],deg2theta:167,deg:490,degener:[3,284],degrad:[8,18,281,356,478],degre:[3,6,8,20,21,24,28,29,32,35,36,38,65,79,92,93,95,97,98,100,102,103,108,114,145,146,147,148,149,150,151,152,153,154,155,156,157,158,160,161,167,168,174,175,178,179,186,188,190,193,206,217,224,231,233,234,239,240,245,255,256,260,261,262,263,274,275,276,278,282,284,298,299,302,317,318,319,324,340,342,346,349,351,363,390,393,401,479,487,490,496],degress:[148,206],del:483,delai:[3,6,12,366,392,487],deleg:402,delet:[2,3,7,8,12,54,57,60,63,166,171,172,197,206,207,209,210,211,212,215,217,228,231,255,300,317,318,337,339,354,364,366,369,424,449,469,470,471,472,480,481,486,491,493,495,496],delete_atom:[],delete_bond:[],delete_el:203,deli:190,delimit:[467,495],deloc:[256,395,440],delr:419,delt_lo:483,delta:[],delta_1:377,delta_3:377,delta_7:377,delta_conf:3,delta_ij:[419,430],delta_mu:3,delta_pi:377,delta_r:430,delta_sigma:377,delta_ua:376,delx:190,delz:190,dem:376,demand:294,demo:11,demon:279,demonstr:[289,419],den:285,dendrim:401,denniston:[9,242,244,245,246,281],denomin:[7,173],denot:[120,224,240,281,292,294,387,400,402,433,437,439],dens:[71,217,395],densiti:[3,6,7,9,18,40,41,59,101,118,128,142,154,166,168,198,199,203,206,210,211,214,220,229,242,245,248,249,281,285,286,290,326,331,358,360,364,371,377,393,419,420,421,430,434,440,444,446,447,448,469,478,479,487,494],density_continu:439,density_summ:439,depart:[0,7],departur:[253,289],depend:[1,2,3,6,8,9,11,12,16,17,18,20,21,22,23,24,25,26,27,28,29,30,31,32,35,38,39,40,41,43,44,45,46,47,48,49,51,53,54,56,61,63,65,68,69,70,71,79,92,93,104,110,111,114,115,116,117,121,142,145,151,155,156,162,168,169,174,175,176,177,178,179,180,182,183,185,186,187,188,190,191,193,194,197,198,199,200,201,204,206,208,209,210,212,213,214,216,218,220,226,227,230,233,234,235,237,239,240,242,244,245,252,255,257,258,259,260,261,262,263,264,265,272,274,275,276,278,280,291,294,296,299,301,302,308,314,317,318,319,321,323,325,326,328,330,331,334,335,336,337,339,340,341,342,343,345,346,349,351,356,358,363,364,366,367,368,370,371,372,374,375,377,378,379,380,381,382,383,384,385,386,387,388,390,391,393,394,395,396,397,398,399,400,401,402,405,407,408,409,410,411,412,413,414,415,416,419,420,422,423,425,426,427,429,430,432,433,434,435,440,441,442,450,451,452,453,454,455,456,457,458,460,461,462,464,466,469,471,472,475,479,481,483,486,487,489,495,496],dependend:6,depflag:12,dephas:[464,483],depos:221,deposit:[],deprec:[290,432],depth:[51,146,193,326,398,434],dequidt:9,der:[87,109,385,386,415,432,433,461,490],deriv:[6,7,8,9,38,56,63,87,142,162,188,207,218,220,231,239,252,255,257,258,259,260,261,262,263,280,286,290,294,323,324,326,331,332,335,362,364,372,377,385,390,395,396,400,409,413,414,419,422,432,433,450,452,461,490],derjagin:461,derlet:280,descend:194,descent:[7,362],descib:[40,193,290],describ:[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17,18,19,38,39,40,41,42,56,62,63,68,70,71,73,88,112,115,118,120,132,142,143,146,147,148,152,153,156,159,161,162,166,167,168,170,171,180,185,188,191,192,197,198,199,206,207,208,209,210,211,212,214,217,218,219,220,221,223,224,232,233,236,237,238,239,240,241,242,244,245,246,250,254,255,256,260,268,277,280,282,287,288,289,290,291,292,299,303,311,314,315,316,317,318,319,320,321,322,323,324,329,331,332,334,339,355,356,358,361,362,363,364,365,369,372,373,375,376,378,379,380,382,383,384,385,386,387,390,393,395,396,398,399,400,402,405,407,408,409,410,411,412,413,414,415,416,417,418,419,422,423,429,430,431,432,433,434,435,440,441,442,449,450,451,452,453,454,455,456,458,460,461,462,464,466,467,469,470,471,472,473,479,482,483,486,495,496,497],descript:[],descriptor:[142,191,403],deserno:356,design:[0,3,6,7,8,9,11,13,14,15,17,120,150,153,167,203,217,223,224,255,256,280,281,300,321,326,373,374,375,376,379,382,387,389,395,415,416,417,420,421,430,433,452,478],desir:[2,3,6,7,11,12,14,15,16,33,40,50,59,71,88,91,114,119,143,150,168,181,190,206,212,218,220,229,231,232,239,240,241,245,255,276,284,285,286,287,290,294,299,302,314,317,318,319,320,325,332,347,352,355,356,358,361,363,364,365,391,393,401,416,417,451,453,455,465,466,467,469,473,478,483,484,486,487,495,496,497],desk:7,desktop:[4,6,7,10,12,193],despit:490,destabil:377,destre:349,destroi:[11,39,215,216],detail:[1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,22,37,40,41,42,55,63,66,67,68,71,75,78,90,91,94,103,105,107,109,111,113,114,116,119,121,142,143,145,146,147,148,151,161,162,163,165,168,169,172,173,176,187,190,191,193,194,197,198,199,203,206,207,208,209,210,212,214,216,217,218,219,220,221,229,231,232,233,234,236,237,239,241,242,246,252,253,254,255,256,257,258,259,260,261,262,263,267,269,274,275,276,277,278,281,284,285,286,288,289,291,292,293,299,302,314,317,318,319,320,321,322,324,325,326,327,328,329,330,337,339,341,350,355,356,359,363,364,366,367,370,371,372,373,375,376,377,379,381,382,383,384,385,386,387,390,391,395,396,398,399,400,401,402,407,408,409,410,411,412,413,414,415,416,417,418,419,423,424,429,432,433,434,440,441,442,450,457,460,461,467,469,470,471,472,474,475,478,479,481,484,487,488,495,496,499],detect:[2,3,12,42,61,63,86,92,230,285,325,365,386,401,406,464,466,469,480,483,495],determ:370,determin:[1,3,6,8,9,12,15,39,40,42,51,57,58,59,61,62,68,71,87,103,109,111,114,120,121,129,143,156,157,166,167,168,190,191,193,194,195,196,200,201,202,205,206,207,208,209,210,211,212,213,214,218,220,221,224,226,231,234,235,237,239,240,245,250,252,253,255,261,262,263,274,275,276,278,280,282,286,289,296,297,298,299,300,301,304,306,308,314,317,318,319,321,327,328,331,332,333,334,335,336,337,350,355,356,358,364,366,367,370,372,373,381,386,390,392,393,397,399,402,403,411,419,422,424,433,434,440,449,452,456,461,466,469,470,472,474,476,479,483,485,486,488,494,495,496],detil:110,devan:[9,435],devanathan:455,develop:[0,3,5,6,7,8,9,11,12,14,15,16,17,18,19,42,236,260,284,289,290,293,372,377,395,421,422,440,458,471],devemi:9,deviat:[253,260,280,397],deviator:9,devic:[1,3,12,15,17,236,370],device_typ:370,devin:[291,386],devis:421,dfactor:193,dff:490,dfft_fftw2:12,dfft_fftw3:12,dfft_fftw:12,dfft_none:12,dfft_singl:[3,12,356],dfft_xxx:12,dfftw:12,dfftw_size:12,dft:[9,293,422],dhi:[59,190,220,285],dhug:[253,289],dhugoniot:[253,289],dia:419,diagnost:[],diagon:[3,6,83,142,143,144,218,255,286,299,329,437,439],diagonalstyl:441,diagram:[41,120,167,187,214,282],diallo:401,diam:[193,194,285,364],diamet:[3,6,40,42,115,168,191,193,194,198,199,239,285,299,314,316,330,332,364,376,385,398,399,409,434,457,461,469,470,479],diamond:[358,395,419],diamter:[40,285],dick:6,dicsuss:252,dictat:[204,253],did:[3,12,363,391,392,393,399,424,453,455,477],didn:3,die:18,diel:[],dielectr:[],diff:[3,6,12,164,328,355],differ:[1,2,3,4,6,7,8,9,10,11,12,14,15,16,17,18,22,37,38,39,41,42,54,55,56,61,64,68,70,71,87,92,95,97,98,122,142,145,146,147,148,149,151,154,155,156,157,158,160,161,162,168,169,171,176,187,188,190,191,193,194,197,199,202,204,206,209,214,215,216,217,218,219,220,224,230,231,232,233,234,235,236,239,240,242,252,255,256,257,258,259,261,262,263,265,267,270,272,273,274,275,278,280,282,284,286,289,290,291,294,297,299,302,303,311,312,314,317,318,319,322,323,324,326,329,330,331,332,335,339,340,350,352,354,355,356,358,359,361,362,364,365,367,368,369,370,371,372,377,381,382,384,385,386,391,393,395,398,399,400,402,405,407,408,410,411,418,419,420,421,423,424,426,430,432,433,434,435,436,437,439,440,441,442,450,451,452,453,455,457,458,461,463,464,466,467,469,471,472,473,474,477,478,479,481,483,484,486,487,488,490,494,495,496,497],differenti:[1,3,6,29,188,355,387,430,454],difficult:[218,282,370,401,478],difficulti:[92,108,302,432],diffract:[],diffus:[],digit:[2,3,194,339,422],dih_table1:188,dih_table2:188,dihedr:[],dihedral_coeff:[],dihedral_cosineshift:27,dihedral_styl:[],dihedralcoeff:3,dihedraltyp:216,dihydrid:395,dij:302,dilat:[],dim1:3,dim2:3,dim:[3,59,71,145,149,150,151,154,155,156,157,158,160,168,190,210,220,237,332,358,419,472,494,495,496],dimdim:495,dimems:281,dimens:[],dimensinon:71,dimension:[3,39,92,114,120,142,145,148,149,150,151,154,155,156,157,158,160,167,189,206,210,254,281,326,358,361,365,430,469,479],dimensionless:[106,123,124,126,129,131,133,138,142,326,356,441,461],dimentionless:137,dimer:[6,299,419],dimgrai:194,dimstr:[41,214],dinola:[286,317],dintel_offload_noaffin:16,dipol:[],dipolar:[4,29,40,191,316,490],dir1:480,dir2:480,dir:[1,3,4,8,9,11,12,253,280,289,313,430,432,433,467,480,495],dirac:142,direc:430,direct:[],directli:[3,6,8,9,11,12,87,115,142,144,191,192,193,200,226,233,237,242,281,300,318,330,332,333,334,335,358,362,370,371,372,378,380,381,387,390,393,395,407,411,424,427,435,449,467,479,480,481,487,495],directoi:14,directori:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,60,195,219,238,284,290,293,310,314,323,324,365,369,371,372,377,384,386,387,393,394,396,403,404,415,419,420,421,422,426,430,431,432,433,440,441,451,453,454,455,458,467,469,470,471,480,495],disabl:[3,12,16,326,406,467,482,495],disadvantag:[6,214],disallow:[191,220,255],disappear:471,discard:[2,3,41,71,208,210,214,327,335,466,471,472],discontinu:[9,188,363,413],discourag:419,discov:[13,327],discret:[6,8,40,42,193,194,239,242,376],discuss:[],disk:[6,84,85,92,161,189,221,231,285,467],disloc:[70,422],disord:[39,70,422],disp:[],dispar:434,disperion:[390,411],dispers:[3,6,7,9,166,281,355,356,381,390,411,416,424,433,452,458],displac:[],displace_atom:[],displace_box:59,displacemet:472,displai:[11,13,22,37,44,55,176,187,191,193,341,350,384,450],dispters:3,disregard:422,dissip:[6,232,239,281,323,324,379,391,399,416,417,450],dissolut:215,dist:[6,69,91,110,119,191,282,298,392,449,464,496],distanc:[],distinct:[6,224,296,355,434],distinguish:[6,86,142,245,376,395,468],distort:371,distrbut:371,distribut:[],distro:[113,384,429,430],ditto:[8,12,14,15,16,17,18,42,117,216,462,467],div:8,divd:119,diverg:[3,12,39,299,324,471,490,497],divid:[3,6,16,41,91,114,119,128,130,143,165,166,176,187,194,206,207,209,214,220,280,322,329,334,355,363,365,396,433,440,458,478,486,495],divis:[6,242,377,405,415,466,487,495],dl_poli:[6,7],dlambda:162,dlammps_async_imd:236,dlammps_bigbig:[12,39],dlammps_ffmpeg:[3,12,193],dlammps_gzip:[3,12,191,193,325,469,470,474],dlammps_jpeg:[3,12,193],dlammps_longlong_to_long:12,dlammps_memalign:[12,16],dlammps_png:[3,12,193],dlammps_smallbig:12,dlammps_smallsmal:12,dlammps_xdr:[12,191],dlen:479,dlmp_intel_offload:[12,16],dlo:[59,190,220,285],dlopen:6,dlvo:[7,385,461],dm_lb:242,dmax:[314,361],dna:7,doc:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,22,37,40,42,55,57,59,63,66,68,75,87,90,94,103,105,106,107,109,111,113,114,116,119,121,143,146,147,148,161,163,165,168,169,170,176,187,190,191,192,193,194,195,197,198,199,204,205,206,207,208,209,210,211,212,221,231,239,240,250,255,256,261,262,263,267,274,275,276,277,278,285,288,299,311,314,317,318,319,328,332,335,337,339,341,350,354,363,364,365,370,371,372,375,376,384,386,387,393,394,396,401,402,404,405,419,420,421,424,426,429,430,431,441,450,451,453,455,457,458,467,469,470,471,472,474,477,478,479,486,487,495,496,497,498],docuement:434,dodd:[42,376],dodgerblu:194,doe:[0,1,2,3,5,6,7,8,9,11,12,14,15,16,17,18,33,38,39,41,42,50,54,56,59,62,63,67,70,71,72,87,88,91,105,112,118,119,120,144,146,148,150,151,156,158,162,167,168,169,170,172,174,176,181,187,188,190,191,192,193,194,197,203,204,206,210,213,214,216,217,218,220,224,226,228,231,232,235,237,239,240,242,245,251,255,256,257,258,259,261,262,263,274,275,276,277,278,286,287,288,292,294,297,299,314,317,319,321,322,326,329,330,331,334,335,336,337,342,343,344,346,347,349,354,355,356,357,358,364,365,366,371,372,373,374,375,376,377,379,381,382,383,385,386,387,388,390,391,392,393,394,395,397,398,399,400,402,403,404,405,406,409,410,412,413,414,416,417,419,420,421,422,424,430,431,432,433,434,436,437,438,439,440,441,442,443,444,445,446,447,448,449,451,452,453,454,455,456,457,458,460,461,462,464,465,466,467,469,470,471,472,473,476,477,479,480,481,482,483,486,487,490,495,499],doegenomestolif:7,doesn:[3,7,8,12,168,191,204,210,211,311,364,366,370,372,386,394,404,432,433,451,453,454,455,458,469,471],dof:[3,8,114,146,147,148,161,206,299,496],dof_per_atom:[148,206],dof_per_chunk:[148,206],doff:[364,469],doi:[6,219],domain:[3,6,7,12,13,18,39,41,42,58,61,62,71,120,157,167,170,190,192,193,194,197,204,214,218,220,221,235,238,242,255,256,282,294,299,326,331,332,355,356,365,370,392,424,464,466,469,473,486],domin:[1,395,483],don:[0,8,11,12,13,118,171,200,226,240,288,335,419,440,467,469],donadio:318,done:[1,3,6,7,8,12,14,15,16,17,18,38,39,41,56,59,62,71,162,165,168,171,188,191,193,194,203,204,206,208,209,210,211,212,214,215,216,217,218,220,221,229,231,236,237,239,240,247,255,261,262,263,274,275,276,278,279,281,282,283,288,296,299,300,302,314,317,318,319,321,323,324,337,339,354,355,356,363,365,366,369,370,372,381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85,287,289,290,291,294,296,298,299,301,303,308,310,317,318,319,322,323,324,326,328,329,331,334,336,337,339,354,358,363,365,366,367,369,370,386,391,397,398,401,405,416,422,423,430,432,433,434,436,437,438,440,441,442,452,457,458,462,465,466,467,469,471,472,476,477,480,483,485,487,495,496],equat:[3,6,7,8,9,91,108,114,120,167,176,187,197,218,224,225,233,239,240,242,245,253,254,255,256,260,276,280,282,289,290,294,302,314,322,326,329,331,332,334,336,349,355,356,385,390,391,395,396,399,404,416,417,419,424,434,437,439,444,445,447,448,462,490],equi:256,equidist:254,equil:[3,290,359,476,499],equilater:479,equilibr:[3,4,5,6,7,9,59,91,168,197,204,207,217,218,231,253,255,256,276,277,289,290,291,292,322,323,324,329,386,387,432,433,465,479],equilibria:329,equilibribum:[215,216],equilibrium:[1,3,4,6,7,21,24,26,27,28,29,32,35,36,38,43,47,48,49,51,53,56,59,151,152,175,177,218,220,231,232,233,240,242,255,260,276,289,290,294,298,302,303,311,314,321,322,324,329,340,342,346,349,386,419,426,440,490],equilibrium_angl:8,equilibrium_dist:8,equilibrium_start:203,equival:[6,12,13,29,59,61,126,127,135,140,166,170,194,209,212,218,220,231,239,255,276,286,298,299,334,391,395,440,453,455,469,472,477,478,487,490],equlibrium:6,equliibr:[290,292],er3:167,eradiu:[40,115,395,469],eras:[301,323],erat:[220,417],erc:387,erfc:[387,407,424],erforc:115,erg:494,erhart:[204,393,453,455],ermscal:373,ernst:9,eror:3,eros:419,erose_form:419,erot:[],errata:[453,455],erratum:331,erron:3,error:[],erta:399,ervel:[115,469],escap:[221,490],especi:[8,11,16,156,168,197,204,214,231,289,294,297,298,370,466],espresso:[9,293],essenti:[8,11,12,27,88,130,149,150,151,154,155,156,157,158,160,177,207,260,281,330,356,372,387,407,455,474,487],essex:29,establish:[87,235],estim:[1,3,6,10,12,38,41,56,91,143,203,214,225,253,314,321,355,356,361,424,433,452,483,487],esu:494,esub:419,eta:[6,242,255,289,290,292,330,394,396,398,430,454,458,494],eta_dot:255,eta_ij:430,eta_ji:396,etag:[40,469],etail:487,etap:255,etap_dot:255,etc:[1,2,3,6,7,8,9,10,11,12,13,15,16,39,40,42,54,61,68,89,90,91,95,111,112,115,117,143,145,148,149,150,151,152,154,155,156,157,158,160,162,168,170,171,172,181,191,193,194,197,198,203,204,205,206,209,210,211,212,215,216,220,221,229,231,232,239,255,285,296,300,326,327,335,339,354,355,363,364,365,366,368,393,394,402,415,417,422,428,432,433,451,453,455,458,464,467,469,470,471,476,478,479,483,485,486,487,488,490,494,495,497,499],ethernet:18,etol:[363,365,464,483],etot0:289,etot:[6,95,97,98,112,143,154,194,224,240,253,289,486,487],eu2:167,eu3:167,euler:[363,365],eulerian:203,euqat:443,europhi:242,ev_tal:8,evalu:[2,3,9,11,12,38,56,71,87,88,91,109,119,142,144,148,158,166,168,190,191,193,194,198,199,200,201,203,205,206,207,208,209,210,211,212,213,220,226,232,234,235,237,238,239,240,281,287,290,301,304,308,317,318,319,328,331,334,336,337,339,355,356,361,363,370,422,424,430,436,438,440,452,464,465,467,471,472,474,476,477,478,479,483,485,487,495,496],evalut:[339,467],evan:[156,276],evanseck:[6,20,174,382,481],evapor:[],evaul:[8,363],evdwl:[109,432,433,487],even:[3,6,8,12,15,17,18,34,39,41,52,57,59,61,63,70,71,121,169,170,184,188,191,194,197,198,199,204,205,206,209,210,211,212,214,215,216,218,220,221,224,237,240,253,255,256,281,294,296,299,300,310,314,322,326,329,331,335,337,348,355,361,363,365,370,375,395,396,399,402,405,424,434,458,459,469,470,472,474,475,476,478,479,481,484,486,487,488,490,499],evenli:[3,41,143,188,214,242,405,459],event:[],eventu:[3,6,12,15,170,290,483],ever:[54,56,238,314],evera:[385,398,434,450],everi:[0,1,2,3,6,8,9,11,12,15,16,39,41,71,72,91,115,121,130,156,171,191,192,193,194,195,197,198,199,200,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,220,221,225,228,229,231,233,235,236,237,242,243,251,255,256,260,279,280,281,285,286,287,288,289,290,291,292,294,296,297,299,300,302,303,314,316,317,318,319,320,321,322,325,326,327,328,329,337,339,354,356,365,366,367,370,391,392,402,415,432,433,440,446,463,464,465,469,471,473,474,476,477,478,483,484,485,487,495,499],everyth:[8,109],everywher:[118,409],eviri:395,evolut:[233,242,282,464],evolv:[242,282,327],ewald:[2,3,5,6,7,8,12,88,112,120,143,327,355,356,363,378,380,381,387,390,395,407,411,427,435,450,452],ewald_disp:390,ewalddisp:3,exact:[22,41,44,71,124,162,171,176,214,217,232,233,239,240,241,285,294,295,314,326,341,355,384,471,476,483,495,497,499],exactli:[3,6,12,14,17,38,41,42,56,59,71,72,91,118,146,152,159,168,188,198,199,209,214,220,225,232,239,240,241,256,268,269,277,281,289,314,319,320,333,370,384,391,393,399,402,416,424,452,471,472,479,483,495],exager:490,examin:[6,8,9,17,217,281],examp:[467,495],exampl:[],exce:[3,6,16,17,18,41,58,71,170,205,206,209,210,211,212,214,218,220,225,228,255,281,296,300,305,306,314,363,370,469,495],exceed:[3,41,59,214,220,255,314,477],excel:395,except:[1,2,5,6,8,9,11,14,20,21,22,23,24,25,26,27,28,29,30,31,32,35,37,38,40,41,43,44,45,46,47,48,49,51,53,54,55,56,59,60,71,89,90,110,111,114,119,143,145,146,147,148,149,150,151,152,154,155,156,157,158,159,160,161,168,172,174,175,176,177,178,179,180,182,183,185,186,187,188,190,191,194,197,200,206,207,209,213,214,218,220,227,230,231,234,237,239,241,255,256,257,258,259,260,261,262,263,264,265,268,269,272,274,275,276,277,278,282,291,292,299,301,302,311,314,317,319,320,326,330,334,337,339,340,341,342,343,345,346,349,350,351,355,356,358,360,364,365,366,368,369,370,371,372,374,378,379,380,381,382,383,384,385,386,387,389,390,391,393,394,395,396,397,398,399,400,401,402,405,407,408,409,410,411,412,413,414,415,416,417,420,425,426,427,429,432,433,434,435,442,450,451,452,453,454,455,457,458,460,461,462,464,466,467,469,471,472,474,477,478,479,480,481,483,487,490,494,495,496,498],excess:[208,395],exchang:[2,3,6,8,9,61,62,197,203,204,231,239,291,299,322,326,329,355,370,395,484],exchange:355,excit:[9,395],exclud:[3,6,9,12,16,17,63,71,114,142,148,155,156,172,191,206,210,215,216,243,251,284,297,299,321,332,337,363,364,366,379,399,402,405,416,417,424,449,481],exclus:[1,3,9,12,16,87,370,386,422,424,478,488],excurs:[255,464],exectubl:12,execut:[1,2,3,4,6,8,11,12,17,60,169,193,236,293,339,354,357,369,465,467,477,480,483,495],exempl:440,exemplari:232,exemplifi:395,exert:[6,237,240,294,333,334,335,356],exhaust:[203,369,495],exhibit:[92,255,362,395,478],exist:[3,6,7,8,11,12,13,16,37,55,59,68,70,124,168,169,187,192,193,194,197,202,213,216,218,221,231,284,285,287,337,340,342,343,344,346,350,359,364,370,402,432,449,459,465,467,469,470,471,480,481,482,495,496,497],exit:[2,3,11,12,41,57,191,214,354,369,467,468,477,486,495],exlanatori:3,exp:[],expand:[],expans:[12,142,191,480,495],expect:[1,3,8,12,13,14,15,16,17,18,19,41,42,71,103,149,160,166,188,214,226,231,233,252,280,286,288,289,294,299,337,356,366,384,419,422,424,464,467,469,471,474,478,483,495],expens:[6,10,71,194,280,284,299,326,337,355,356,366,370,467],experi:[6,13,15,17,213,221,236,245,254,286,298,299,361,365,391,424,478,483],experienc:[6,12,244,245],experiment:[231,355,370,483],expert:12,expertis:7,explain:[1,3,6,8,9,11,12,16,18,41,59,63,65,68,69,71,72,73,76,77,79,86,93,148,156,188,191,193,194,197,206,207,212,214,216,218,220,255,280,288,299,311,337,339,354,355,358,364,365,369,375,393,405,440,442,457,467,470,471,474,476,479,490,495,499],explan:[3,6,59,115,142,191,206,254,280,402,463,466,467,469,478],explanatori:[3,8,119,191,205,206,209,210,211,299,364,466,495],explantori:[3,295],explic:423,explicit:[6,9,11,22,44,77,87,115,118,162,176,198,199,220,305,306,341,360,372,373,377,382,384,393,395,406,416,456,463,466,470,473],explicitli:[3,6,8,12,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,43,45,46,47,48,49,51,53,54,56,71,111,114,145,155,158,166,168,174,175,177,178,179,180,182,183,185,186,188,191,194,200,210,213,220,227,230,232,234,239,255,257,258,259,260,261,262,263,264,265,272,274,275,276,278,288,289,291,299,301,302,317,319,320,326,330,334,340,342,343,345,346,349,351,364,370,371,372,374,378,379,380,381,382,383,384,385,386,387,388,390,391,392,393,394,396,397,398,399,400,401,402,405,406,407,408,409,410,411,412,413,414,415,416,420,422,424,425,426,427,429,434,435,442,443,444,445,446,447,448,450,451,452,453,454,455,456,457,458,460,461,462,469,471,472,478,479,481,482,488,490],explictli:[16,482],exploit:[9,15,17,282],explor:[120,167],expon:[3,290,292,393,398,401,415,423,435],exponenti:[87,430,451,458,462,483,495],expos:11,exposit:[203,391,392],express:[6,142,154,168,198,199,218,252,280,290,326,332,339,377,393,395,409,419,440,441,450,495],expressiont:377,extend:[],extens:[3,6,9,17,44,45,46,53,55,63,82,83,84,87,88,91,95,98,99,109,111,119,121,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,197,200,201,204,212,213,219,222,226,229,230,231,233,234,235,237,239,241,253,255,260,269,280,281,297,298,299,301,303,308,311,313,317,318,319,320,321,323,324,326,328,331,335,336,398,419,422,433,434,441,486,487],extent:[1,3,41,42,45,57,71,166,170,191,202,210,214,237,333,336,355,358,372,436,438,452,466,469,472],exterior:[3,6,335],extern:[],extra:[3,6,8,12,16,17,40,41,46,61,71,103,111,112,114,120,143,145,146,147,149,151,154,155,156,157,158,160,161,167,168,169,170,174,194,209,214,216,255,287,288,289,299,314,363,364,367,368,390,399,402,405,419,424,466,467,469,472,481,490,495],extract:[3,6,11,13,36,63,87,109,117,119,121,198,199,292,365,387,396,419,441,467,474,486],extract_atom:11,extract_comput:[11,467],extract_fix:11,extract_glob:11,extract_vari:11,extramak:[12,15],extrapol:1,extrem:[1,3,6,17,58,193,208,218,220,255,324,395,454,490],extrema:415,extrins:203,f77:[5,7,12],f90:[5,7,12],f_1:6,f_5:[164,328],f_a:[453,454,455],f_ave:119,f_c:454,f_f:455,f_fix_id:289,f_harm:324,f_i:[29,430],f_id:[6,71,119,121,191,197,205,206,207,208,209,210,211,212,250,316,328,487,495],f_ij:430,f_indent:212,f_int:323,f_j:29,f_jj:91,f_k:430,f_langevin:326,f_max:[289,294],f_msst:253,f_r:[240,453,454,455],f_sigma:377,f_solid:324,f_ss:6,f_temp:[],face:[3,6,57,59,71,156,166,170,202,210,211,331,333,334,335,336,358,398,419,434,469,472],face_threshold:166,facet:166,facil:[0,12],facilit:[6,13,42],fact:[6,8,16,233,314,324,399,440,481],factor:[1,3,6,12,18,24,28,32,35,36,39,41,46,47,57,58,59,72,87,91,103,110,117,118,120,142,162,167,170,174,185,190,191,193,194,198,199,207,214,218,220,221,231,236,239,241,242,253,255,256,260,282,286,290,298,302,304,306,314,318,322,329,330,331,335,346,356,358,364,370,372,373,377,378,380,382,387,388,389,391,395,399,402,406,407,419,422,424,426,427,433,435,442,451,456,466,469,472,473,478,481,483,484,487,490,494,495],factori:[3,467],factoriz:355,fail:[3,11,12,59,172,218,221,355,363,365,389,433,467],failur:[123,437,468,495],fairli:[11,424,478,483],faken:73,falcon:236,fall:[3,6,194,209,285,467,495],fals:[86,337,339,440,495],fame:8,famili:[458,466],familiar:[0,11],fan:430,far:[3,6,12,17,57,59,61,86,191,194,195,214,215,216,218,221,255,280,298,299,314,331,342,346,361,365,366,457,467,469,474,487],farago:239,farrel:[453,455],farther:191,fashion:[6,8,41,71,168,194,197,198,199,204,210,214,216,221,231,233,237,252,253,255,257,258,259,260,261,262,263,271,274,275,276,277,278,288,289,291,299,303,307,313,316,324,326,330,331,332,334,336,365,402,416,472,481,495,498],fasolino:404,fast:[6,7,9,12,13,17,39,191,266,289,327,355,356,379,416,417,422,450,452,471,476,478,487,496,499],faster:[1,6,9,10,11,12,14,15,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,61,63,106,111,114,145,155,174,175,177,178,179,180,182,183,185,186,188,191,194,200,213,214,220,227,230,234,238,239,255,257,258,259,260,261,262,263,264,265,272,274,275,276,278,286,290,291,299,301,302,314,317,319,321,323,326,330,334,340,342,343,345,346,349,351,355,356,367,368,370,371,372,374,377,378,379,380,381,382,383,384,385,386,387,390,391,393,394,396,397,398,399,400,401,402,405,407,408,409,410,411,412,413,414,415,416,420,425,426,427,429,434,435,442,450,451,452,453,454,455,457,458,460,461,462,464,472,478,482,490],fastest:[1,6,14,17,156,210,326,327,370,466],fatal:[3,486],fault:[70,433],faulti:12,fava:398,favor:217,favorit:7,fbmc:321,fcc:[],fcm:[271,495],fdirect:224,fdotr:403,fdti:87,fe2:167,fe3:167,fe_md_boundari:203,featu:8,featur:[],fecr:393,feedback:[7,236],feel:[7,236,237,245,280,335,337,365,424],felling:421,felt:335,femtosecond:494,fene:[],fennel:[387,407],fep:[],ferguson:[6,174,481],fermi:[1,12,15,154,370,455],fermion:[9,395],fernando:418,ferrand:[9,13],few:[1,3,4,5,6,7,9,10,11,12,13,14,18,39,195,205,206,207,209,210,211,212,240,255,285,288,290,302,328,355,363,364,365,372,440,466,469,474,478,480,488,495,497],fewer:[1,3,11,15,16,61,245,478],fewest:3,fextern:229,feynman:282,fff:467,ffield:[386,396,432,433,440],ffmpeg:[3,12,193],ffplai:193,fft:[1,3,7,12,14,15,88,111,112,143,281,355,356,478],fft_inc:[12,356],fft_lib:12,fft_path:12,fftbench:[355,488],fftw2:12,fftw3:12,fftw:[11,12],fhg:[7,9],ficiti:449,fictiti:[6,200,201,226,229,233,282,298,387,407,411,449],field1:[470,474],field2:470,field:[],fifth:[311,426],figur:[1,3,8,11,12,289,466,467],fij:390,file0:280,file1:[11,13,280,325,339,364,474,476,480],file2:[11,13,325,339,364,474,476,480],file:[],file_from:192,filen:364,filenam:[3,12,13,38,41,56,188,191,193,194,195,203,206,207,208,209,210,211,212,214,219,280,284,287,290,291,292,295,296,299,300,325,326,352,353,354,364,365,371,372,377,387,393,394,396,404,419,420,421,426,430,431,432,433,440,441,451,452,453,454,455,458,465,466,467,470,471,476,480,487,495,497,498,499],filennam:476,filep:[3,191,194,471,476,499],filepo:296,fill:[7,9,168,193,285,326,358,366,377,422,433,472],filter:[194,203],final_integr:8,final_integrate_respa:8,finchham:[6,150,389],find:[0,3,4,6,7,8,11,12,13,14,16,38,39,56,61,71,73,87,119,171,188,195,204,217,218,228,231,254,280,286,294,298,361,363,365,366,387,402,407,411,419,440,450,452,490,495],find_custom:8,fine:[16,17,172,200,226,324,366,370,495],finer:[142,168,495],finest:355,finger:[168,190,252,472],finish:[6,11,41,214,339,352,354,355,367,369,370,457,474,495,496],finit:[],finni:[7,393,450],finvers:224,fiorin:[9,219],fire:[],firebrick:194,first:[0,1,2,3,5,6,8,9,11,12,14,15,16,17,21,38,39,41,42,45,46,54,56,57,59,61,62,71,81,88,91,104,105,106,108,114,118,119,129,132,135,136,140,143,153,156,162,164,166,167,169,170,171,175,188,191,192,193,194,195,197,198,206,207,209,210,211,212,214,217,220,231,232,237,242,252,253,254,255,280,282,287,288,289,291,296,299,302,303,311,312,314,315,316,323,324,325,326,328,332,337,339,340,347,358,363,364,365,366,369,370,371,372,375,377,378,380,382,384,386,387,393,395,396,399,400,402,403,404,405,406,407,411,416,417,419,421,422,424,426,430,432,433,440,441,449,451,452,453,454,455,458,462,464,465,466,467,469,470,471,474,476,478,481,482,483,486,487,490,495,496,497,499],fischer:[6,9,19,20,174,382,481],fit:[3,6,9,12,38,56,188,298,314,372,377,404,419,424,445,452,454,477,495],five:[73,154,289,364,377,420,469,483],fix:[],fix_adapt:[162,199,415],fix_atom_swap:[],fix_bal:62,fix_deposit:[3,204,285],fix_evapor:204,fix_flux:203,fix_gcmc:[204,364],fix_gl:233,fix_gld:233,fix_grav:285,fix_id:[3,218,253,255,257,258,259,260,261,262,263,286,289],fix_modifi:[],fix_mov:[190,332],fix_nh:8,fix_npt:233,fix_nvt:[204,231],fix_poem:[3,6],fix_pour:[3,221],fix_qbmsst:9,fix_qeq:[3,386],fix_rattl:302,fix_reax_bond:432,fix_rigid:[245,375],fix_saed_vtk:300,fix_setforc:8,fix_shak:302,fix_srd:3,fix_styl:260,fix_temp_rescal:320,fixedpoint:[218,255],fixextern:229,fixid:203,fji:390,flag1:[223,368],flag2:[223,368],flag:[3,8,11,12,14,15,16,17,40,66,74,75,81,86,89,90,94,104,105,107,120,163,167,171,191,193,194,195,212,217,219,223,236,239,243,245,251,252,281,288,299,311,313,314,321,325,334,337,353,356,364,368,369,370,372,401,406,419,422,449,464,466,467,469,470,471,473,474,475,479,495],flag_buck:381,flag_coul:[381,390,411],flag_lj:[390,411],flagfld:[379,416,417],flaghi:[3,379,416,417],flaglog:[379,416,417],flagn:223,flagvf:[379,416,417],flat:[6,326,331,332,336],flavor:[2,7,12],fld:[9,331,379,416,417],flen:373,flex_press:373,flexibl:[3,6,8,169,193,206,210,219,233,256,322,329,395,454,487],flip:[3,6,220,255,333,334],floor:495,flop:12,floralwhit:194,flow:[],fluctuat:[6,64,87,218,231,232,239,242,255,260,280,281,324,326,349],fluid:[],fluid_veloc:246,flush:[3,194,486],flux:[],flv:193,fly:[7,9,12,41,193,197,203,208,221,224,299,302,327,377,422,487,490],fmackai:9,fmag:222,fmass:282,fmax:[363,487],fmomentum:224,fmsec:[2,194,239,240,252,255,286,299,317,318,478,489,494,496],fname:354,fno:[12,16],fnorm:[363,487],fnpt:224,fnvt:224,foce:402,fock:373,focu:302,fogarti:[9,292,433],foil:[142,280,441],fold:[312,478],folk:7,follow:[0,1,2,3,4,6,7,8,9,11,12,13,14,15,16,17,18,19,20,23,24,25,26,27,28,29,30,31,32,35,36,38,41,42,43,45,46,47,48,49,51,53,54,56,59,63,64,70,71,73,91,92,97,98,108,115,118,119,121,142,143,146,147,148,154,156,161,164,166,168,169,174,177,178,179,180,182,183,185,186,188,191,192,193,194,197,203,204,205,206,207,208,209,210,211,212,214,219,220,221,224,225,229,231,232,233,236,238,239,240,242,245,253,255,260,261,262,263,274,275,276,278,281,282,284,287,288,289,290,292,294,296,298,299,300,302,316,317,318,319,322,323,324,325,326,328,329,337,338,342,343,344,345,346,349,351,353,358,360,363,364,365,370,371,372,373,374,375,376,377,378,379,380,381,382,383,385,386,387,388,389,390,391,392,393,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,423,424,425,426,427,429,430,431,432,433,434,435,437,439,440,441,442,443,444,445,446,447,448,449,451,452,453,454,455,456,457,458,460,461,462,464,466,467,469,470,472,474,476,477,478,481,483,484,485,490,495,496,498],foo:[4,8,11,12,191,193,229,467,480,495],foot:6,footprint:[12,370],fopenmp:[12,16,18],forc:[],force_uvm:17,forceatom:245,forcefield:[298,401],forcegroup:242,forcezero:361,ford:390,forestgreen:194,forev:71,forget:[240,490],forgiv:255,fork:[12,191],form:[2,3,6,8,12,19,22,44,54,63,66,74,75,77,81,87,89,90,92,94,104,105,107,118,142,143,162,163,172,176,194,197,198,199,216,232,233,239,241,245,252,276,281,292,294,298,299,326,331,335,340,341,344,349,360,362,364,365,372,373,377,384,393,395,397,401,402,406,418,419,421,422,426,427,430,432,433,434,440,441,442,450,452,453,454,455,461,463,466,467,469,474,479,486,490,495],formal:[6,78,80,91,232,233,239,255,282,314,322,440],format:[2,3,6,7,8,9,12,13,22,38,41,44,56,68,77,176,188,191,192,193,194,195,206,209,210,211,212,214,216,281,284,288,290,292,295,299,300,310,325,326,337,338,341,360,364,365,371,372,377,384,393,396,406,419,421,431,432,433,435,441,452,458,459,466,467,469,470,471,474,485,486,487,495,497],former:[6,12,16,39,41,194,214,326,330,377,379,475,481,495],formerli:[7,13],formul:[1,40,64,143,200,226,239,255,276,290,292,298,302,325,355,372,377,393,395,398,419,429],formula:[2,3,6,7,13,21,22,37,44,54,55,70,73,87,89,90,91,95,97,98,107,114,120,143,145,146,147,148,149,150,151,152,154,155,156,157,158,159,160,161,167,168,173,175,176,187,190,191,198,199,200,201,206,207,208,209,212,213,220,226,234,235,237,239,240,252,280,281,287,296,301,308,312,314,317,318,319,328,331,334,336,337,339,340,341,343,350,358,364,372,373,375,377,382,383,384,385,390,391,393,394,398,399,400,401,403,406,407,409,410,411,413,414,416,417,419,423,424,425,434,435,442,450,451,453,454,455,458,460,461,465,469,472,479,486,487,494,495,496],forth:[1,6,11,12,13,14,15,369,467,472,476],fortran:[3,6,9,11,12,13,229,393,402,419,432,433],fortun:8,forward:[3,8,87,354,365,370],foster:[377,429,430],foul:171,found:[3,6,9,12,73,162,191,217,219,231,236,242,281,321,327,339,354,366,384,387,390,464,470,471,486],four:[6,11,54,81,104,105,142,164,253,326,349,364,365,422,464],fourier:[],fourth:[6,106,298,311,321,382,426,440],fox:[6,120,174,448,481],fphi:[38,56,452],fpic:12,fplo:[38,56,452],fprime:452,fqdn:238,fqq:390,frac:[],fraction:[1,3,6,8,12,16,39,41,80,111,143,171,190,193,194,204,215,216,217,218,253,285,289,296,297,314,319,320,358,365,370,377,379,399,416,417,474,479],fragment:[42,236,296],fraig:[42,376],frame:[83,142,194,203,253,289,333,398],framer:[193,194],framework:[5,233,371,441],franc:9,fraunhof:9,free:[5,6,7,9,13,29,60,63,70,87,162,199,280,314,323,324,325,326,362,365,373,395,415,422,430,461,466],freedom:[3,6,8,95,97,98,100,102,103,114,145,146,147,148,149,150,151,152,153,154,155,156,157,158,16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roup:245,innermost:[38,56,71,368,452,478],innernod:245,innner:413,inordin:327,inorgan:[6,458],inp:[219,339,441,458],input1:[65,68,69,79,93,110,115,116,117,119,121,316],input2:[65,68,69,79,93,110,115,116,117,119,121,316],input:[],input_doubl:3,inquir:304,insensit:12,insert:[3,5,7,8,12,59,168,197,221,231,237,285,355,441,449,467,473,490],insid:[2,3,6,8,11,71,131,137,168,191,194,205,210,211,221,222,228,231,237,242,245,285,299,314,331,333,334,335,336,337,353,358,409,467,468,469,471,472,479,483,495],insight:[6,13],instabl:[242,390,439],instal:[],instanc:[6,11,198,219,233,333,397,402,424,430,467,490],instantan:[6,63,217,218,232,233,255,260,281,286,289,294,296,299,321,475,487],instanti:[6,11,12,203,402,466],instead:[1,3,6,8,9,11,12,13,17,18,40,41,59,61,63,70,71,90,104,119,146,150,172,188,191,199,206,209,210,211,212,214,218,219,231,239,242,245,246,281,287,297,299,316,334,353,355,356,359,366,370,380,381,393,406,408,415,419,422,464,472,476,483,485,490,495],institut:[9,236,284],instruct:[],insuffici:[3,6,12],insult:255,insur:[3,6,11,12,17,39,40,61,73,103,105,168,169,188,191,193,194,200,215,216,221,226,227,228,229,231,234,239,251,287,288,297,299,314,326,331,335,336,337,339,354,364,366,370,385,398,402,428,434,452,466,467,469,470,474,477,478,486,487,495,496],int_max:3,integ:[3,6,8,11,12,39,40,42,64,68,70,71,108,115,117,119,121,142,166,168,171,172,174,178,179,183,188,190,191,193,194,204,206,210,211,215,216,217,221,223,229,231,232,233,236,239,240,241,242,281,284,285,288,289,294,299,314,316,318,321,325,326,345,355,358,379,391,392,405,419,432,433,437,439,441,464,466,467,468,469,477,478,479,483,486,495,496],integr:[],integrate_ulsph:[],intel:[],intel_cpu:[12,16],intel_phi:[12,16],intend:[3,6,8,12,13,36,208,232,431,469],intens:[1,3,6,9,63,66,74,75,86,89,90,91,94,104,105,106,107,114,116,118,119,120,121,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,163,164,165,167,197,206,207,209,210,211,212,214,215,216,217,225,228,235,245,253,255,260,296,299,300,314,322,326,328,329,486,487],intepol:495,inter:[14,18,42,61,62,148,171,172,191,217,239,241,254,291,299,355,365,377,479,490,495,497,499],interact:[1,3,6,7,8,9,10,11,12,14,15,16,17,22,29,33,37,39,42,44,50,54,55,57,61,63,65,69,72,77,79,87,88,92,93,108,109,110,112,114,117,118,124,125,126,127,129,130,131,132,133,134,135,137,138,139,140,142,143,144,146,147,161,162,166,169,170,171,172,173,174,176,180,181,187,191,197,198,199,215,216,217,230,231,236,237,239,241,245,269,280,282,284,290,292,298,299,305,306,314,315,321,326,330,331,332,335,336,341,342,343,344,346,350,355,356,363,364,365,366,367,368,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,427,429,430,433,434,435,437,439,440,441,442,449,450,451,453,454,455,456,457,458,459,460,461,462,464,467,469,471,473,474,478,479,481,486,487,490,497],interatom:[3,4,7,168,191,254,323,324,371,377,393,395,403,419,422,440,454,495],intercept:120,interchang:6,interconnect:18,interconvert:395,intereract:39,interesect:335,interest:[1,5,7,8,9,11,13,71,167,282,321,324,356,394,417,432,433,467,495],interf:370,interfac:[],interfer:[12,255,372],interg:[6,490],intergr:[478,482],interi:417,interior:[3,6,41,335,472],interlac:419,interleav:[6,168,477],intermedi:[6,12,59,193,254,280,349,365,467,468,477,481],intermix:464,intermolecular:372,intern:[0,2,3,5,6,9,11,16,20,21,24,28,32,35,36,39,40,42,63,87,100,102,120,143,148,150,167,175,188,193,194,197,198,199,203,216,220,224,236,248,249,253,255,260,281,299,303,340,342,346,349,353,363,364,443,444,452,467,469,471,474,483,486,487,494,495,496,497],internal_element_set:203,internal_quadratur:203,internet:238,interpenetr:419,interpentr:[444,445,447],interpol:[6,15,38,56,101,188,193,194,203,242,280,355,356,365,377,424,433,446,452,453],interpret:[2,6,11,193,209,399,442,464,467,483,495],interrupt:289,intersect:[3,6,120,194,335,337,472],intersert:335,interspers:363,interstiti:[166,422],intertia:[3,94],interv:[3,6,91,192,207,239,255,289,294,295,306,440,446,464,483,495],intestieti:120,intial:[6,370,372],intiial:[41,474],intiti:[3,313],intra:299,intra_energi:231,intramolecular:[29,231],introduc:[6,9,92,108,193,255,289,294,299,349,355,371,387,395,407,411,415,451,483,495],introduct:[],intsal:[],intuit:358,inv:[120,167,300],invalid:[3,12,71,89,171,269,365,416,417,471],invari:[108,135,140,142],invent:302,invers:[],invert:[1,6,172,281],invis:335,invoc:[166,217,370,437,439,467],invok:[1,3,6,7,8,11,12,13,14,16,17,18,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,41,43,45,46,47,48,49,51,53,54,56,59,63,66,71,74,75,81,87,88,89,90,94,104,105,107,111,112,113,114,119,145,155,162,163,166,168,169,171,172,174,175,177,178,179,180,182,183,185,186,188,191,193,194,195,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,220,221,222,223,225,226,227,228,229,230,231,232,234,235,236,237,239,240,241,242,243,244,245,246,247,248,249,251,252,254,255,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:[7,41,62,170,214,231,358,469,471,473],rectilinear:[120,167],rector:53,recurs:[41,214,377,457],recust:41,recv:466,red:[2,10,193,194,217,282],redefin:[3,471,477,495],redirect:12,redo:12,reduc:[],reduct:[18,19,119,120,167,253,289,355],redund:396,ree:445,reed:[253,289],rees:[7,9,13],ref:[323,324,362],refactor:6,refer:[],referenc:[3,6,12,63,68,71,116,191,197,207,212,231,288,328,356,387,401,426,434,467,487,495],reflect:[],reformat:7,refresh:203,reg:472,regard:[6,59,252,302,307,429,433],regardless:[15,71,168,171,190,209,210,220,239,255,257,258,259,261,262,263,286,299,308,314,370,466,472,479],regim:[6,322,329,388,478],region:[],region_spher:8,region_styl:335,regist:[8,118,144,310,432,433],regoin:6,regress:495,regspher:168,regstrip:337,regul:6,regular:[1,3,9,41,62,88,166,170,191,193,204,214,231,326,356,388,405,466,469,471,473],reigon:495,reinhardt:[323,324],reject:[168,217,432,484],rel:[1,6,14,27,36,41,59,71,92,104,124,132,142,146,150,151,153,168,177,194,197,204,210,214,220,221,224,231,237,240,251,252,276,280,285,294,296,297,303,311,314,316,321,322,326,333,337,355,356,363,395,398,399,416,417,419,434,461,470,478,483,487,490,496],relat:[],relatic:[],relationship:[6,290,339,355,440,461,490,495],relax:[],releas:[0,5,7,8,13,215],relect:[3,424],reles:42,relev:[2,6,12,41,78,80,113,130,168,172,194,198,199,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,220,221,222,225,227,228,230,231,232,235,236,242,243,244,246,247,248,249,251,252,254,264,265,266,267,268,269,270,271,272,273,279,283,284,285,287,288,291,293,295,296,297,300,301,302,303,308,312,314,315,316,321,322,325,326,327,328,329,330,331,332,333,334,336,337,355,363,373,374,379,385,387,388,390,391,392,395,397,398,399,400,401,406,408,409,410,412,413,414,416,417,424,425,429,434,442,449,452,460,461,462,466,482,496],reli:[3,12,291,395,433,462,469,479],reloc:12,remain:[7,12,33,37,41,50,55,59,71,87,105,148,149,150,151,155,156,157,158,160,171,181,187,188,191,198,199,204,206,207,210,211,218,220,239,240,247,255,256,261,262,263,274,275,276,278,283,284,306,314,317,318,319,325,326,337,339,347,350,364,377,395,402,415,422,424,450,464,469,470,474,479,481,483,487,490,495,496],remaina:377,remaind:[168,191,221,285,314,327,455,469],remap:[3,6,12,59,61,71,151,168,190,210,220,237,252,276,355,469,470,471],remedi:[6,490],rememb:2,remov:[2,3,6,8,9,13,54,71,72,77,92,108,116,118,142,146,147,148,149,150,151,155,156,157,158,160,161,168,171,172,197,206,210,215,228,239,240,245,251,253,255,261,262,263,274,275,276,278,284,290,299,300,302,314,317,318,319,321,337,355,365,390,417,422,469,472,480,481,495,496],remove_bia:8,remove_bias_al:8,remove_molecul:203,remove_sourc:203,remove_speci:203,ren:167,renam:[12,338,480],render:[12,13,191,193,194],rendon:[255,256],reneighbor:[3,8,12,39,57,71,210,214,231,314,327,337,391,486,487],renssela:284,renumb:71,reorder:[3,12,39,466],repeat:[2,6,193,194,210,217,218,231,307,358,377,453,455,457,464,483],repeatedli:2,repel:237,repes:191,replac:[2,3,6,11,12,41,63,89,90,119,145,146,147,148,149,150,151,154,155,156,157,158,160,161,191,193,194,195,206,207,209,210,211,212,214,217,221,239,260,287,294,296,387,409,470,471,476,477,487,495,496,497,499],replic:[],replica:[],replica_fil:12,report:[],repositori:[7,12,403,431,432,433],reprens:326,repres:[1,3,6,8,9,12,15,40,41,42,59,67,71,90,115,118,180,188,191,193,206,207,208,209,210,211,212,218,224,232,234,239,242,255,282,284,286,294,299,300,303,311,326,328,335,356,365,371,377,398,405,415,416,417,419,420,421,427,430,432,433,456,457,464,466,469,479,481,484,490,495,497],represent:[3,6,8,9,57,59,136,170,191,232,233,282,326,377,395,398,422,434,469,472,490],reprocess:474,reproduc:[3,255,332,387,393,399],repul:419,repuls:[6,7,9,36,40,45,46,110,237,290,331,332,335,372,376,377,385,387,391,395,399,401,415,419,423,440,449,455,458,461,462,479],reqir:[290,292],request:[3,6,8,12,41,104,171,188,191,236,242,297,314,316,353,355,424,432,433,464,474,479,483,495,496,497],requir:[],rerun:[],rescal:[],research:[5,7,242,246,422,464,483],resembl:294,reserv:[12,236,490],reservoir:[91,231,235,239,326],reset:[],reset_atomic_reference_posit:203,reset_dt:8,reset_target:8,reset_tim:203,reset_timestep:[],resid:13,residu:236,residue1:366,resist:[6,236],resolut:[208,440,452],resolv:[218,282,314,417],resort:3,resourc:[7,371,393],respa:[3,16,225,236,255,368,371,372,373,374,375,376,377,378,379,380,381,382,383,385,386,387,388,390,391,392,393,394,395,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,416,417,418,419,420,421,422,423,425,427,429,431,432,433,434,435,440,441,442,443,444,445,446,447,448,449,451,452,453,454,455,457,458,460,461,462,477,478,489,495],respecifi:422,respect:[1,6,9,10,13,14,15,17,20,21,23,24,25,26,27,28,29,30,31,32,35,38,40,42,43,45,46,47,48,49,51,53,54,56,59,70,71,87,89,97,98,111,114,120,124,145,150,153,155,162,166,167,174,175,177,178,179,180,182,183,185,186,188,193,194,210,211,216,217,218,220,234,237,239,240,242,255,257,258,259,260,261,262,263,264,265,272,274,275,276,278,290,291,299,300,303,311,313,326,331,334,340,342,343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9,301,302,303,311,313,314,315,317,318,319,320,322,323,324,325,326,328,329,330,331,332,334,335,336,337,339,340,342,343,345,346,347,349,351,354,355,356,358,360,362,363,364,365,366,369,370,371,372,374,377,378,379,380,381,382,383,384,385,386,387,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,419,420,421,422,424,425,426,427,428,429,430,431,432,433,434,435,440,441,442,443,444,445,446,447,448,449,451,452,453,454,455,457,458,460,461,462,463,464,465,466,467,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,486,487,488,490,494,495,496,497,499],young:[399,436,438],your:[0,1,2,3,4,5,6,7,8,11,12,13,14,15,16,17,18,19,20,21,23,24,25,26,27,28,29,30,31,32,35,38,39,40,43,45,46,47,48,49,51,53,54,56,59,61,109,111,114,118,145,146,147,151,155,161,166,168,169,170,171,172,174,175,177,178,179,180,182,183,185,186,188,190,191,192,193,200,203,207,209,212,213,215,216,217,218,220,221,227,230,231,234,236,239,252,255,257,258,259,260,261,262,263,264,265,272,274,275,276,278,285,288,291,297,299,301,302,303,316,317,319,322,326,328,329,330,331,332,334,335,336,337,340,342,343,345,346,349,351,356,358,364,365,366,369,370,371,372,374,377,378,379,380,381,382,383,384,385,386,387,390,391,392,393,394,396,397,398,399,400,401,402,403,404,405,407,408,409,410,411,412,413,414,415,416,419,420,421,422,424,425,426,427,429,430,432,433,434,435,442,449,451,452,453,454,455,457,458,460,461,462,463,466,467,469,471,472,473,476,477,478,479,480,481,482,486,487,494,495,497,499],yourself:[6,8,12,13,218,364],yplane:332,ypo:168,ysu:[3,191,316,470],yuan:9,yukawa:[],yukawa_1_1:459,yxz:466,yzx:466,z_i:[395,455,462],z_j:[455,462],z_meam:419,zachari:13,zannoni:398,zbl:[],zblcut:455,zblcutinn:441,zblcutout:441,zblexpscal:455,zblz:441,zcm:299,zcylind:332,zepeda:204,zero:[3,4,6,9,11,12,26,27,39,41,48,49,59,61,63,66,71,72,75,87,88,90,92,94,103,104,105,106,107,108,110,111,112,114,115,116,117,118,119,120,123,142,143,146,147,148,149,156,157,160,161,163,165,166,167,168,170,171,172,174,177,186,188,190,191,193,194,197,198,199,200,202,204,205,206,207,208,209,210,211,212,213,214,215,216,218,220,225,226,227,228,230,231,232,233,235,239,240,241,242,243,245,251,252,253,255,260,269,272,282,287,288,289,290,291,294,296,297,299,300,301,302,305,306,308,314,316,321,322,324,326,329,330,331,332,333,334,336,337,338,339,345,358,361,363,364,365,366,370,373,377,378,380,381,382,385,387,390,391,395,398,400,401,402,403,407,409,411,412,415,417,418,419,422,424,429,433,434,435,440,449,452,456,458,462,464,465,466,469,470,472,474,476,477,478,479,483,484,487,490,495,496,497,499],zeta:[3,242,290,396],zfactor:193,zflag:[155,156,243,245,251,299,321],zhang:[299,322,399],zhi:[3,6,170,191,202,325,331,334,336,469,472,487],zhi_bound:[6,191],zhou:[13,377,396,430,453,455],zhu:448,ziegenhain:13,ziegler:[284,419,450,455,462],zimmerman2004:203,zimmerman2010:203,zimmerman:[9,70,203,377],zlat:[220,237,487],zlib:191,zlim:440,zlo:[3,6,170,191,202,325,331,333,334,336,469,472,487],zlo_bound:[6,191],zmax:[202,242,495],zmin:[242,495],zn2:167,zone:[120,300],zoom:[3,191,193,194],zorig:71,zplane:332,zr4:167,zrest:313,zsu:[3,191,316,470],zwall:331,zwall_veloc:242,zxy:466,zybin:433,zyx:466},titles:["LAMMPS Documentation","5. Accelerating LAMMPS performance","3. Commands","12. Errors","7. Example problems","13. Future and history","6. How-to discussions","1. Introduction","10. Modifying & extending LAMMPS","4. Packages","8. Performance & scalability","11. Python interface to LAMMPS","2. Getting Started","9. Additional tools","5.USER-CUDA package","5.GPU package","5.USER-INTEL package","5.KOKKOS package","5.USER-OMP package","5.OPT package","angle_style charmm command","angle_style class2 command","angle_coeff command","angle_style cosine command","angle_style cosine/delta command","angle_style cosine/periodic command","angle_style cosine/shift command","angle_style cosine/shift/exp command","angle_style cosine/squared command","angle_style dipole command","angle_style fourier command","angle_style fourier/simple command","angle_style harmonic command","angle_style hybrid command","angle_style none command","angle_style quartic command","angle_style sdk command","angle_style command","angle_style table command","atom_modify command","atom_style command","balance command","Body particles","bond_style class2 command","bond_coeff command","bond_style fene command","bond_style fene/expand command","bond_style harmonic command","bond_style harmonic/shift command","bond_style harmonic/shift/cut command","bond_style hybrid command","bond_style morse command","bond_style none command","bond_style nonlinear command","bond_style quartic command","bond_style command","bond_style table command","boundary command","box command","change_box command","clear command","comm_modify command","comm_style command","compute command","compute ackland/atom command","compute angle/local command","compute angmom/chunk command","compute basal/atom command","compute body/local command","compute bond/local command","compute centro/atom command","compute chunk/atom command","compute cluster/atom command","compute cna/atom command","compute com command","compute com/chunk command","compute contact/atom command","compute coord/atom command","compute damage/atom command","compute dihedral/local command","compute dilatation/atom command","compute displace/atom command","compute erotate/asphere command","compute erotate/rigid command","compute erotate/sphere command","compute erotate/sphere/atom command","compute event/displace command","compute fep command","compute group/group command","compute gyration command","compute gyration/chunk command","compute heat/flux command","compute hexorder/atom command","compute improper/local command","compute inertia/chunk command","compute ke command","compute ke/atom command","compute ke/atom/eff command","compute ke/eff command","compute ke/rigid command","compute meso_e/atom command","compute meso_rho/atom command","compute meso_t/atom command","compute_modify command","compute msd command","compute msd/chunk command","compute msd/nongauss command","compute omega/chunk command","compute orientorder/atom command","compute pair command","compute pair/local command","compute pe command","compute pe/atom command","compute plasticity/atom command","compute pressure command","compute property/atom command","compute property/chunk command","compute property/local command","compute rdf command","compute reduce command","compute saed command","compute slice command","compute smd/contact_radius command","compute smd/damage command","compute smd/hourglass_error command","compute smd/internal_energy command","compute smd/plastic_strain command","compute smd/plastic_strain_rate command","compute smd/rho command","compute smd/tlsph_defgrad command","compute smd/tlsph_dt command","compute smd/tlsph_num_neighs command","compute smd/tlsph_shape command","compute smd/tlsph_strain command","compute smd/tlsph_strain_rate command","compute smd/tlsph_stress command","compute smd/triangle_mesh_vertices","compute smd/ulsph_num_neighs command","compute smd/ulsph_strain command","compute smd/ulsph_strain_rate command","compute smd/ulsph_stress command","compute smd/vol command","compute sna/atom command","compute stress/atom command","compute force/tally command","compute temp command","compute temp/asphere command","compute temp/body command","compute temp/chunk command","compute temp/com command","compute temp/cs command","compute temp/deform command","compute temp/deform/eff command","compute temp/drude command","compute temp/eff command","compute temp/partial command","compute temp/profile command","compute temp/ramp command","compute temp/region command","compute temp/region/eff command","compute temp/rotate command","compute temp/sphere command","compute ti command","compute torque/chunk command","compute vacf command","compute vcm/chunk command","compute voronoi/atom command","compute xrd command","create_atoms command","create_bonds command","create_box command","delete_atoms command","delete_bonds command","dielectric command","dihedral_style charmm command","dihedral_style class2 command","dihedral_coeff command","dihedral_style cosine/shift/exp command","dihedral_style fourier command","dihedral_style harmonic command","dihedral_style helix command","dihedral_style hybrid command","dihedral_style multi/harmonic command","dihedral_style nharmonic command","dihedral_style none command","dihedral_style opls command","dihedral_style quadratic command","dihedral_style command","dihedral_style table command","dimension command","displace_atoms command","dump command","dump h5md command","dump image command","dump_modify command","dump molfile command","echo command","fix command","fix adapt command","fix adapt/fep command","fix addforce command","fix addtorque command","fix append/atoms command","fix atc command","fix atom/swap command","fix ave/atom command","fix ave/chunk command","fix ave/correlate command","fix ave/correlate/long command","fix ave/histo command","fix ave/spatial command","fix ave/spatial/sphere command","fix ave/time command","fix aveforce command","fix balance command","fix bond/break command","fix bond/create command","fix bond/swap command","fix box/relax command","fix colvars command","fix deform command","fix deposit command","fix drag command","fix drude command","fix drude/transform/direct command","fix dt/reset command","fix efield command","fix enforce2d command","fix evaporate command","fix external command","fix freeze command","fix gcmc command","fix gld command","fix gle command","fix gravity command","fix heat command","fix imd command","fix indent command","fix ipi command","fix langevin command","fix langevin/drude command","fix langevin/eff command","fix lb/fluid command","fix lb/momentum command","fix lb/pc command","fix lb/rigid/pc/sphere command","fix lb/viscous command","fix lineforce command","fix meso command","fix meso/stationary command","fix_modify command","fix momentum command","fix move command","fix msst command","fix neb command","fix nvt command","fix nvt/eff command","fix nph/asphere command","fix nph/body command","fix nph/sphere command","fix nphug command","fix npt/asphere command","fix npt/body command","fix npt/sphere command","fix nve command","fix nve/asphere command","fix nve/asphere/noforce command","fix nve/body command","fix nve/eff command","fix nve/limit command","fix nve/line command","fix nve/noforce command","fix nve/sphere command","fix nve/tri command","fix nvt/asphere command","fix nvt/body command","fix nvt/sllod command","fix nvt/sllod/eff command","fix nvt/sphere command","fix oneway command","fix orient/fcc command","fix phonon command","fix pimd command","fix planeforce command","fix poems","fix pour command","fix press/berendsen command","fix print command","fix property/atom command","fix qbmsst command","fix qeq/point command","fix qeq/comb command","fix qeq/reax command","fix qmmm command","fix qtb command","fix reax/bonds command","fix reax/c/species command","fix recenter command","fix restrain command","fix rigid command","fix saed/vtk command","fix setforce command","fix shake command","fix smd command","fix smd/adjust_dt command","fix smd/integrate_tlsph command","fix smd/integrate_ulsph command","fix smd/move_tri_surf command","fix smd/setvel command","<no title>","fix smd/wall_surface command","fix spring command","fix spring/rg command","fix spring/self command","fix srd command","fix store/force command","fix store/state command","fix temp/berendsen command","fix temp/csvr command","fix temp/rescale command","fix temp/rescale/eff command","fix tfmc command","fix thermal/conductivity command","fix ti/rs command","fix ti/spring command","fix tmd command","fix ttm command","fix tune/kspace command","fix vector command","fix viscosity command","fix viscous command","fix wall/lj93 command","fix wall/gran command","fix wall/piston command","fix wall/reflect command","fix wall/region command","fix wall/srd command","group command","group2ndx command","if command","improper_style class2 command","improper_coeff command","improper_style cossq command","improper_style cvff command","improper_style distance command","improper_style fourier command","improper_style harmonic command","improper_style hybrid command","improper_style none command","improper_style ring command","improper_style command","improper_style umbrella command","include command","info command","jump command","kspace_modify command","kspace_style command","label command","lattice command","log command","mass command","min_modify command","min_style command","minimize command","molecule command","neb command","neigh_modify command","neighbor command","newton command","next command","package command","pair_style adp command","pair_style airebo command","pair_style awpmd/cut command","pair_style beck command","pair_style body command","pair_style body/rounded/polygon command","pair_style bop command","pair_style born command","pair_style brownian command","pair_style buck command","pair_style buck/long/coul/long command","pair_style lj/charmm/coul/charmm command","pair_style lj/class2 command","pair_coeff command","pair_style colloid command","pair_style comb command","pair_style coul/cut command","pair_style coul/diel command","pair_style born/coul/long/cs command","pair_style lj/cut/dipole/cut command","pair_style dpd command","pair_style dsmc command","pair_style eam command","pair_style edip command","pair_style eff/cut command","pair_style eim command","pair_style gauss command","pair_style gayberne command","pair_style gran/hooke command","pair_style lj/gromacs command","pair_style hbond/dreiding/lj command","pair_style hybrid command","pair_style kim command","pair_style lcbop command","pair_style line/lj command","pair_style list command","pair_style lj/cut command","pair_style lj96/cut command","pair_style lj/cubic command","pair_style lj/expand command","pair_style lj/long/coul/long command","pair_style lj/sf command","pair_style lj/smooth command","pair_style lj/smooth/linear command","pair_style lj/cut/soft command","pair_style lubricate command","pair_style lubricateU command","pair_style lj/mdf command","pair_style meam command","pair_style meam/spline","pair_style meam/sw/spline","pair_style mgpt command","pair_style mie/cut command","pair_modify command","pair_style morse command","pair_style nb3b/harmonic command","pair_style nm/cut command","pair_style none command","pair_style peri/pmb command","pair_style polymorphic command","pair_style quip command","pair_style reax command","pair_style reax/c command","pair_style resquared command","pair_style lj/sdk command","pair_style smd/hertz command","pair_style smd/tlsph command","pair_style smd/tri_surface command","pair_style smd/ulsph command","pair_style smtbq command","pair_style snap command","pair_style soft command","pair_style sph/heatconduction command","pair_style sph/idealgas command","pair_style sph/lj command","pair_style sph/rhosum command","pair_style sph/taitwater command","pair_style sph/taitwater/morris command","pair_style srp command","pair_style command","pair_style sw command","pair_style table command","pair_style tersoff command","pair_style tersoff/mod command","pair_style tersoff/zbl command","pair_style thole command","pair_style tri/lj command","pair_style vashishta command","pair_write command","pair_style yukawa command","pair_style yukawa/colloid command","pair_style zbl command","partition command","prd command","print command","processors command","python command","quit command","read_data command","read_dump command","read_restart command","region command","replicate command","rerun command","reset_timestep command","restart command","run command","run_style command","set command","shell command","special_bonds command","suffix command","tad command","temper command","thermo command","thermo_modify command","thermo_style command","timer command","timestep command","<no title>","uncompute command","undump command","unfix command","units command","variable command","velocity command","write_data command","write_dump command","write_restart command"],titleterms:{"break":215,"default":[37,39,40,55,57,58,59,61,62,71,87,88,92,103,104,106,108,109,120,124,125,142,148,156,157,161,167,168,171,173,187,189,190,191,193,194,195,196,198,199,200,202,203,204,206,210,211,212,215,216,218,219,220,221,225,228,231,232,237,239,240,241,242,243,245,250,253,255,256,260,276,277,281,282,285,286,287,288,289,291,294,296,297,299,300,314,316,321,322,323,324,327,329,331,333,337,350,353,355,356,358,359,361,362,364,366,367,368,370,373,377,379,395,416,417,422,424,432,433,449,450,464,465,466,469,470,472,474,476,477,478,481,483,485,486,487,488,489,494,496,497,498],"function":495,"long":[208,378,380,381,382,383,387,389,390,407,411,415,427,435],"new":8,"static":12,acceler:1,ackland:64,acknowledg:7,adapt:[198,199],addforc:200,addit:[12,13],addtorqu:201,adiabat:6,adjust_dt:304,adp:371,airebo:372,alloi:393,amber2lmp:13,amber:6,angl:[8,65],angle_coeff:22,angle_styl:[2,20,21,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38],angmom:66,append:202,arrai:6,aspher:[6,82,146,257,261,265,266,274],atc:[9,203],atom:[6,7,8,64,67,70,71,72,73,76,77,78,80,81,85,92,96,97,100,101,102,108,112,113,115,142,143,166,202,204,205,288,495],atom_modifi:39,atom_styl:40,attract:5,aug:[],aveforc:213,awpmd:[9,373],balanc:[41,214],barostat:6,basal:67,beck:374,berendsen:[286,317],between:6,binary2txt:13,bodi:[6,8,42,68,147,258,262,267,275,375,376],bond:[8,13,69,215,216,217,295],bond_coeff:44,bond_styl:[2,43,45,46,47,48,49,50,51,52,53,54,55,56],bop:377,born:[378,389],boundari:[7,57],box:[6,58,218],brownian:379,buck:[380,381,389,418],bug:3,build:[9,11,12],calcul:6,call:12,categori:2,centro:70,ch2lmp:13,chain:13,change_box:59,charmm:[6,20,174,382,415],chunk:[6,66,71,75,90,94,105,107,116,148,163,165,206],citat:7,class2:[21,43,175,340,383],clear:60,cluster:72,cmm:9,cna:73,code:6,coeffici:6,colloid:[331,385,461],colvar:[9,13,219],com:[74,75,149],comb3:386,comb:[291,386],come:5,comm_modifi:61,comm_styl:62,comman:[],command:[2,6,8,12,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,491,492,493,494,495,496,497,498,499],common:3,comparison:1,compos:6,compress:9,comput:[2,6,8,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,495],compute_modifi:103,condit:7,conduct:[6,322],constant:6,constraint:7,contact:76,contact_radiu:122,coord:77,core:6,correl:[207,208],cosin:[23,24,25,26,27,28,177],cossq:342,coul:[378,380,381,382,383,387,388,389,400,407,411,415,427,435],coupl:6,creat:216,create_atom:168,create_bond:169,create_box:170,createatom:13,creation:7,csld:318,csvr:318,cubic:409,cuda:[9,14,111,114,145,155,200,213,227,230,234,255,264,301,302,317,319,330,378,380,382,383,393,399,400,407,408,410,413,425,451,453],custom:8,cut:[49,373,380,383,387,390,395,397,407,408,415,423,427],cvff:343,damag:[78,123],data2xmovi:13,data:6,databas:13,deby:[387,407],dec:[],deform:[151,152,220],delete_atom:171,delete_bond:172,delta:24,deposit:221,descript:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,491,492,493,494,495,496,497,498,499],diagnost:7,diel:388,dielectr:173,diffract:9,diffus:6,dihedr:[8,79],dihedral_coeff:176,dihedral_styl:[2,174,175,177,178,179,180,181,182,183,184,185,186,187,188],dilat:80,dimens:189,dipol:[6,29,390],direct:224,discuss:6,disp:6,displac:[81,86],displace_atom:190,distanc:344,distribut:[7,12],document:0,dpd:391,drag:222,dreid:[6,401],drude:[6,9,153,223,224,240],dsf:[387,407],dsmc:392,dump:[6,8,191,192,193,195],dump_modifi:194,dynam:290,eam:[13,393],echo:196,edip:394,eff:[9,13,97,98,152,154,159,241,256,268,277,320,395],efield:226,eim:396,elast:6,emac:13,enforce2d:227,ensembl:7,erot:[82,83,84,85],error:3,evapor:228,event:86,exampl:[1,4,6,11,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,482,483,484,485,486,487,488,489,491,492,493,494,495,496,497,498,499],exp:[27,177],expand:[46,410],extend:[8,11],extern:229,fcc:280,featur:[7,8,495],fene:[45,46],fep:[9,13,87,199],field:[6,7],file:6,finit:6,fire:290,fix:[2,6,8,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,495],fix_modifi:[198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,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ir:[6,109,110],pair_coeff:384,pair_modifi:424,pair_styl:[2,371,372,373,374,375,376,377,378,379,380,381,382,383,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,460,461,462],pair_writ:459,pairwis:8,parallel:11,paramet:6,pars:2,partial:155,particl:[6,7,42],partit:463,past:5,per:6,perform:[1,10],peri:429,period:25,phonon:[9,13,281],pimd:282,piston:333,planeforc:283,plastic:113,plastic_strain:126,plastic_strain_r:127,pmb:429,poem:[9,284],point:290,polariz:6,poli:[379,416,417],polygon:376,polym:13,polymorph:430,post:7,potenti:[2,6,8],pour:285,pppm:6,prd:464,pre:7,press:286,pressur:114,previou:12,print:[287,465],problem:[3,4],process:[6,7],processor:466,profil:156,properti:[6,115,116,117,288],pymol_aspher:13,python:[9,11,13,467],qbmsst:289,qeq:[290,291,292],qmmm:[9,293],qtb:[9,294],quadrat:186,quantiti:6,quartic:[35,54],quip:431,quit:468,ramp:157,rattl:302,rdf:118,read_data:469,read_dump:470,read_restart:471,reax:[9,13,292,295,296,432,433],reaxc:9,rebo:372,recent:297,reduc:119,refer:495,reflect:334,region:[8,119,158,159,335,472,495],relat:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,35,36,37,38,40,41,43,44,45,46,47,48,49,50,51,53,54,55,56,57,59,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,83,84,85,86,87,89,91,92,93,94,95,96,97,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,185,186,187,188,189,190,191,192,193,194,195,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,228,230,231,232,233,234,235,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,283,284,285,286,287,288,289,290,291,292,294,295,296,297,299,300,301,303,304,305,306,307,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,349,350,351,352,353,354,355,356,358,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,429,430,431,432,433,434,435,436,437,438,439,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,474,475,476,477,478,479,481,482,483,484,485,486,487,488,489,491,492,493,495,496,497,498,499],relax:218,replic:473,replica:[6,7],report:3,requir:12,rerun:474,rescal:[319,320],reset:225,reset_timestep:475,resquar:434,restart2data:13,restart:[6,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,218,219,220,221,222,224,225,226,227,228,229,230,231,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,283,284,285,286,287,288,289,290,291,292,293,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,328,329,330,331,332,333,334,335,336,476],restrain:298,restrict:[14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,491,492,493,494,495,496,497,498,499],rho:128,rhosum:446,rigid:[6,83,99,245,299],ring:349,rotat:160,round:376,rule:2,run:[6,11,12,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,218,219,220,221,222,224,225,226,227,228,229,230,231,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,283,284,285,286,287,288,289,290,291,292,293,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,328,329,330,331,332,333,334,335,336,477],run_styl:478,scalabl:10,scalar:6,screen:12,script:[2,6,8,11],sdk:[36,435],self:313,serial:11,set:[6,479],setforc:301,setvel:308,shake:302,share:[11,12],shell:[6,480],shield:290,shift:[26,27,48,49,177],simpl:31,simul:6,size:6,slater:290,slice:121,sllod:[276,277],small:299,smd:[9,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,303,304,305,306,307,308,310,436,437,438,439],smooth:[413,414],smtbq:[9,440],sna:142,snad:142,snap:441,snapshot:6,snav:142,soft:[415,442],solver:2,sourc:7,spatial:[210,211],spc:6,speci:296,special:[7,424,495],special_bond:481,sph:[9,443,444,445,446,447,448],sphere:[84,85,161,211,245,259,263,272,278],spheric:6,spline:[420,421],spring:[311,312,313,324],squar:28,srd:[314,336],srp:449,standard:9,start:[12,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,218,219,220,221,222,224,225,226,227,228,229,230,231,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,283,284,285,286,287,288,289,290,291,292,293,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,328,329,330,331,332,333,334,335,336],state:316,stationari:249,stop:[198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,218,219,220,221,222,224,225,226,227,228,229,230,231,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,283,284,285,286,287,288,289,290,291,292,293,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,328,329,330,331,332,333,334,335,336],store:[315,316],strategi:1,streitz:387,stress:[143,144],structur:2,style:[1,2,6,8],submit:8,suffix:482,summari:6,swap:[204,217],syntax:[20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,281,282,283,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409,410,411,412,413,414,415,416,417,418,419,420,421,422,423,424,425,426,427,428,429,430,431,432,433,434,435,436,437,438,439,440,441,442,443,444,445,446,447,448,449,450,451,452,453,454,455,456,457,458,459,460,461,462,463,464,465,466,467,468,469,470,471,472,473,474,475,476,477,478,479,480,481,482,483,484,485,486,487,488,489,491,492,493,494,495,496,497,498,499],system:6,tabl:[0,6,38,56,188,452,453],tad:483,taitwat:[447,448],talli:144,temp:[145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,317,318,319,320],temper:484,temperatur:6,tersoff:[453,454,455],test:11,tfmc:321,thermal:[6,322],thermo:[6,485],thermo_modifi:486,thermo_styl:487,thermodynam:[6,8],thermostat:6,thole:456,time:[6,212],timer:488,timestep:489,tip3p:6,tip4p:[6,387,407,411,415],tip:12,tlsph:437,tlsph_defgrad:129,tlsph_dt:130,tlsph_num_neigh:131,tlsph_shape:132,tlsph_strain:133,tlsph_strain_rat:134,tlsph_stress:135,tmd:325,tool:[12,13],torqu:163,transform:224,tri:[273,457],tri_surfac:438,triangle_mesh_vertic:136,triclin:6,tstat:391,ttm:326,tune:327,type:7,ulsph:439,ulsph_num_neigh:137,ulsph_strain:138,ulsph_strain_r:139,ulsph_stress:140,umbrella:351,uncomput:491,undump:492,unfix:493,unit:494,user:[9,12,14,16,18],vacf:164,valu:[6,495],variabl:[6,8,495],variou:1,vashishta:458,vcm:165,vector:[6,328,495],veloc:496,version:[0,5,12],via:12,vim:13,viscos:[6,329],viscou:[246,330],visual:6,vol:141,voronoi:[9,166],vtk:300,wall:[6,331,332,333,334,335,336],wall_surfac:310,warn:3,water:6,weight:209,what:[7,12],wolf:[378,387],wrapper:11,write:6,write_data:497,write_dump:498,write_restart:499,xmgrace:13,xmovi:13,xrd:167,xtc:9,yukawa:[460,461],zbl:[455,462]}})
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