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Steve Plimpton
2016-09-13 17:15:15 -06:00
parent 25e518a4f4
commit c744b23c4c
145 changed files with 1620 additions and 1466 deletions
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2
doc/html/Manual.html
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@ -135,7 +135,7 @@
<H1></H1><div class="section" id="lammps-documentation">
<h1>LAMMPS Documentation</h1>
<div class="section" id="sep-2016-version">
<h2>7 Sep 2016 version</h2>
<h2>13 Sep 2016 version</h2>
</div>
<div class="section" id="version-info">
<h2>Version info:</h2>

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doc/html/Section_commands.html
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@ -247,15 +247,15 @@ inside the parenthesis is treated as an &#8220;immediate&#8221; variable and
evaluated as an <a class="reference internal" href="variable.html"><span class="doc">equal-style variable</span></a>. This is a way
to use numeric formulas in an input script without having to assign
them to variable names. For example, these 3 input script lines:</p>
<pre class="literal-block">
variable X equal (xlo+xhi)/2+sqrt(v_area)
<div class="highlight-default"><div class="highlight"><pre><span></span>variable X equal (xlo+xhi)/2+sqrt(v_area)
region 1 block $X 2 INF INF EDGE EDGE
variable X delete
</pre>
</pre></div>
</div>
<p>can be replaced by</p>
<pre class="literal-block">
region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span>region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE
</pre></div>
</div>
<p>so that you do not have to define (or discard) a temporary variable X.</p>
<p>Note that neither the curly-bracket or immediate form of variables can
contain nested $ characters for other variables to substitute for.

20
doc/html/Section_example.html
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@ -303,11 +303,11 @@ longer times, e.g. to measure a particular quantity.</p>
</tbody>
</table>
<p>Here is how you can run and visualize one of the sample problems:</p>
<pre class="literal-block">
cd indent
cp ../../src/lmp_linux . # copy LAMMPS executable to this dir
lmp_linux -in in.indent # run the problem
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">cd</span> <span class="n">indent</span>
<span class="n">cp</span> <span class="o">../../</span><span class="n">src</span><span class="o">/</span><span class="n">lmp_linux</span> <span class="o">.</span> <span class="c1"># copy LAMMPS executable to this dir</span>
<span class="n">lmp_linux</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">indent</span> <span class="c1"># run the problem</span>
</pre></div>
</div>
<p>Running the simulation produces the files <em>dump.indent</em> and
<em>log.lammps</em>. You can visualize the dump file of snapshots with a
variety of 3rd-party tools highlighted on the
@ -321,17 +321,17 @@ ImageMagick or QuickTime or various Windows-based tools. See the
<a class="reference internal" href="dump_image.html"><span class="doc">dump image</span></a> doc page for more details. E.g. this
Imagemagick command would create a GIF file suitable for viewing in a
browser.</p>
<pre class="literal-block">
% convert -loop 1 *.jpg foo.gif
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">%</span> <span class="n">convert</span> <span class="o">-</span><span class="n">loop</span> <span class="mi">1</span> <span class="o">*.</span><span class="n">jpg</span> <span class="n">foo</span><span class="o">.</span><span class="n">gif</span>
</pre></div>
</div>
</div>
<hr class="docutils" />
<div class="section" id="uppercase-directories">
<h2>7.2. Uppercase directories</h2>
<table border="1" class="docutils">
<colgroup>
<col width="11%" />
<col width="89%" />
<col width="10%" />
<col width="90%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td>ASPHERE</td>

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doc/html/Section_tools.html
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@ -204,7 +204,7 @@ own sub-directories with their own Makefiles.</p>
<li><a class="reference internal" href="#eff"><span class="std std-ref">eff</span></a></li>
<li><a class="reference internal" href="#emacs"><span class="std std-ref">emacs</span></a></li>
<li><a class="reference internal" href="#fep"><span class="std std-ref">fep</span></a></li>
<li><a class="reference internal" href="#ipi"><span class="std std-ref">i-pi</span></a></li>
<li><a class="reference internal" href="fix_ipi.html#ipi"><span class="std std-ref">i-pi</span></a></li>
<li><a class="reference internal" href="#ipp"><span class="std std-ref">ipp</span></a></li>
<li><a class="reference internal" href="#kate"><span class="std std-ref">kate</span></a></li>
<li><a class="reference internal" href="#arc"><span class="std std-ref">lmp2arc</span></a></li>

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@ -128,9 +128,9 @@
<span id="index-0"></span><h1>atom_modify command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
atom_modify keyword values ...
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_modify</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
</pre></div>
</div>
<ul class="simple">
<li>one or more keyword/value pairs may be appended</li>
<li>keyword = <em>id</em> or <em>map</em> or <em>first</em> or <em>sort</em></li>
@ -146,11 +146,11 @@ atom_modify keyword values ...
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
atom_modify map hash
atom_modify map array sort 10000 2.0
atom_modify first colloid
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_modify</span> <span class="nb">map</span> <span class="nb">hash</span>
<span class="n">atom_modify</span> <span class="nb">map</span> <span class="n">array</span> <span class="n">sort</span> <span class="mi">10000</span> <span class="mf">2.0</span>
<span class="n">atom_modify</span> <span class="n">first</span> <span class="n">colloid</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

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doc/html/atom_style.html
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@ -128,9 +128,9 @@
<span id="index-0"></span><h1>atom_style command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
atom_style style args
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_style</span> <span class="n">style</span> <span class="n">args</span>
</pre></div>
</div>
<ul class="simple">
<li>style = <em>angle</em> or <em>atomic</em> or <em>body</em> or <em>bond</em> or <em>charge</em> or <em>dipole</em> or <em>dpd</em> or <em>electron</em> or <em>ellipsoid</em> or <em>full</em> or <em>line</em> or <em>meso</em> or <em>molecular</em> or <em>peri</em> or <em>smd</em> or <em>sphere</em> or <em>tri</em> or <em>template</em> or <em>hybrid</em></li>
</ul>
@ -150,15 +150,15 @@ args = none for any style except the following
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
atom_style atomic
atom_style bond
atom_style full
atom_style body nparticle 2 10
atom_style hybrid charge bond
atom_style hybrid charge body nparticle 2 5
atom_style template myMols
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_style</span> <span class="n">atomic</span>
<span class="n">atom_style</span> <span class="n">bond</span>
<span class="n">atom_style</span> <span class="n">full</span>
<span class="n">atom_style</span> <span class="n">body</span> <span class="n">nparticle</span> <span class="mi">2</span> <span class="mi">10</span>
<span class="n">atom_style</span> <span class="n">hybrid</span> <span class="n">charge</span> <span class="n">bond</span>
<span class="n">atom_style</span> <span class="n">hybrid</span> <span class="n">charge</span> <span class="n">body</span> <span class="n">nparticle</span> <span class="mi">2</span> <span class="mi">5</span>
<span class="n">atom_style</span> <span class="n">template</span> <span class="n">myMols</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

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doc/html/body.html
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@ -247,11 +247,11 @@ mentioned above, the <a class="reference internal" href="fix_rigid.html"><span c
duplicates its functionality.</p>
<p>The atom_style body command for this body style takes two additional
arguments:</p>
<pre class="literal-block">
atom_style body nparticle Nmin Nmax
Nmin = minimum # of sub-particles in any body in the system
Nmax = maximum # of sub-particles in any body in the system
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_style</span> <span class="n">body</span> <span class="n">nparticle</span> <span class="n">Nmin</span> <span class="n">Nmax</span>
<span class="n">Nmin</span> <span class="o">=</span> <span class="n">minimum</span> <span class="c1"># of sub-particles in any body in the system</span>
<span class="n">Nmax</span> <span class="o">=</span> <span class="n">maximum</span> <span class="c1"># of sub-particles in any body in the system</span>
</pre></div>
</div>
<p>The Nmin and Nmax arguments are used to bound the size of data
structures used internally by each particle.</p>
<p>When the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command reads a data file for this
@ -313,11 +313,11 @@ used for 2d models. One example use of this body style is for 2d
discrete element models, as described in <a class="reference internal" href="#fraige"><span class="std std-ref">Fraige</span></a>. Similar to
body style <em>nparticle</em>, the atom_style body command for this body
style takes two additional arguments:</p>
<pre class="literal-block">
atom_style body rounded/polygon Nmin Nmax
Nmin = minimum # of vertices in any body in the system
Nmax = maximum # of vertices in any body in the system
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_style</span> <span class="n">body</span> <span class="n">rounded</span><span class="o">/</span><span class="n">polygon</span> <span class="n">Nmin</span> <span class="n">Nmax</span>
<span class="n">Nmin</span> <span class="o">=</span> <span class="n">minimum</span> <span class="c1"># of vertices in any body in the system</span>
<span class="n">Nmax</span> <span class="o">=</span> <span class="n">maximum</span> <span class="c1"># of vertices in any body in the system</span>
</pre></div>
</div>
<p>The Nmin and Nmax arguments are used to bound the size of data
structures used internally by each particle.</p>
<p>When the <a class="reference internal" href="read_data.html"><span class="doc">read_data</span></a> command reads a data file for this

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@ -128,9 +128,9 @@
<span id="index-0"></span><h1>change_box command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
change_box group-ID parameter args ... keyword args ...
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">parameter</span> <span class="n">args</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">args</span> <span class="o">...</span>
</pre></div>
</div>
<ul class="simple">
<li>group-ID = ID of group of atoms to (optionally) displace</li>
<li>one or more parameter/arg pairs may be appended</li>
@ -175,10 +175,10 @@ parameter = <em>x</em> or <em>y</em> or <em>z</em> or <em>xy</em> or <em>xz</em>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
change_box all xy final -2.0 z final 0.0 5.0 boundary p p f remap units box
change_box all x scale 1.1 y volume z volume remap
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span> <span class="n">xy</span> <span class="n">final</span> <span class="o">-</span><span class="mf">2.0</span> <span class="n">z</span> <span class="n">final</span> <span class="mf">0.0</span> <span class="mf">5.0</span> <span class="n">boundary</span> <span class="n">p</span> <span class="n">p</span> <span class="n">f</span> <span class="n">remap</span> <span class="n">units</span> <span class="n">box</span>
<span class="n">change_box</span> <span class="nb">all</span> <span class="n">x</span> <span class="n">scale</span> <span class="mf">1.1</span> <span class="n">y</span> <span class="n">volume</span> <span class="n">z</span> <span class="n">volume</span> <span class="n">remap</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -223,15 +223,15 @@ will be re-shrink-wrapped before the change_box command completes.
Instead you could do something like this, assuming the simulation box
is non-periodic and atoms extend from 0 to 20 in all dimensions:</p>
</div>
<pre class="literal-block">
change_box all x final -10 20
create_atoms 1 single -5 5 5 # this will fail to insert an atom
</pre>
<pre class="literal-block">
change_box all x final -10 20 boundary f s s
create_atoms 1 single -5 5 5
change_box boundary s s s # this will work
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span> <span class="n">x</span> <span class="n">final</span> <span class="o">-</span><span class="mi">10</span> <span class="mi">20</span>
<span class="n">create_atoms</span> <span class="mi">1</span> <span class="n">single</span> <span class="o">-</span><span class="mi">5</span> <span class="mi">5</span> <span class="mi">5</span> <span class="c1"># this will fail to insert an atom</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span> <span class="n">x</span> <span class="n">final</span> <span class="o">-</span><span class="mi">10</span> <span class="mi">20</span> <span class="n">boundary</span> <span class="n">f</span> <span class="n">s</span> <span class="n">s</span>
<span class="n">create_atoms</span> <span class="mi">1</span> <span class="n">single</span> <span class="o">-</span><span class="mi">5</span> <span class="mi">5</span> <span class="mi">5</span>
<span class="n">change_box</span> <span class="n">boundary</span> <span class="n">s</span> <span class="n">s</span> <span class="n">s</span> <span class="c1"># this will work</span>
</pre></div>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Unlike the earlier &#8220;displace_box&#8221; version of this command, atom
@ -295,30 +295,30 @@ used following a keyword that changed the volume, which is any of the
<em>x</em>, <em>y</em>, <em>z</em> keywords. If the preceding keyword &#8220;key&#8221; had a <em>volume</em>
style, then both it and the current keyword apply to the keyword
preceding &#8220;key&#8221;. I.e. this sequence of keywords is allowed:</p>
<pre class="literal-block">
change_box all x scale 1.1 y volume z volume
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span> <span class="n">x</span> <span class="n">scale</span> <span class="mf">1.1</span> <span class="n">y</span> <span class="n">volume</span> <span class="n">z</span> <span class="n">volume</span>
</pre></div>
</div>
<p>The <em>volume</em> style changes the associated dimension so that the
overall box volume is unchanged relative to its value before the
preceding keyword was invoked.</p>
<p>If the following command is used, then the z box length will shrink by
the same 1.1 factor the x box length was increased by:</p>
<pre class="literal-block">
change_box all x scale 1.1 z volume
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span> <span class="n">x</span> <span class="n">scale</span> <span class="mf">1.1</span> <span class="n">z</span> <span class="n">volume</span>
</pre></div>
</div>
<p>If the following command is used, then the y,z box lengths will each
shrink by sqrt(1.1) to keep the volume constant. In this case, the
y,z box lengths shrink so as to keep their relative aspect ratio
constant:</p>
<pre class="literal-block">
change_box all&quot;x scale 1.1 y volume z volume
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span><span class="s2">&quot;x scale 1.1 y volume z volume</span>
</pre></div>
</div>
<p>If the following command is used, then the final box will be a factor
of 10% larger in x and y, and a factor of 21% smaller in z, so as to
keep the volume constant:</p>
<pre class="literal-block">
change_box all x scale 1.1 z volume y scale 1.1 z volume
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">change_box</span> <span class="nb">all</span> <span class="n">x</span> <span class="n">scale</span> <span class="mf">1.1</span> <span class="n">z</span> <span class="n">volume</span> <span class="n">y</span> <span class="n">scale</span> <span class="mf">1.1</span> <span class="n">z</span> <span class="n">volume</span>
</pre></div>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">For solids or liquids, when one dimension of the box is

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doc/html/compute_dipole_chunk.html
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@ -181,11 +181,11 @@ and how they are set for each atom. You can reset the image flags
<p>The simplest way to output the results of the compute com/chunk
calculation to a file is to use the <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a>
command, for example:</p>
<pre class="literal-block">
compute cc1 all chunk/atom molecule
compute myChunk all dipole/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
<span class="n">compute</span> <span class="n">myChunk</span> <span class="nb">all</span> <span class="n">dipole</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myChunk</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span> <span class="n">mode</span> <span class="n">vector</span>
</pre></div>
</div>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global array where the number of rows = the
number of chunks <em>Nchunk</em> as calculated by the specified <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command. The number of columns =

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doc/html/compute_inertia_chunk.html
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@ -177,11 +177,11 @@ how they are set for each atom. You can reset the image flags
<p>The simplest way to output the results of the compute inertia/chunk
calculation to a file is to use the <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a>
command, for example:</p>
<pre class="literal-block">
compute cc1 all chunk/atom molecule
compute myChunk all inertia/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
<span class="n">compute</span> <span class="n">myChunk</span> <span class="nb">all</span> <span class="n">inertia</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myChunk</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span> <span class="n">mode</span> <span class="n">vector</span>
</pre></div>
</div>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global array where the number of rows = the
number of chunks <em>Nchunk</em> as calculated by the specified <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command. The number of columns =

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doc/html/compute_ke_atom_eff.html
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@ -168,11 +168,11 @@ eFF.</p>
thermodynamic output by using the <a class="reference internal" href="thermo_modify.html"><span class="doc">thermo_modify</span></a>
command, as shown in the following example:</p>
</div>
<pre class="literal-block">
compute effTemp all temp/eff
thermo_style custom step etotal pe ke temp press
thermo_modify temp effTemp
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">effTemp</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">eff</span>
<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">etotal</span> <span class="n">pe</span> <span class="n">ke</span> <span class="n">temp</span> <span class="n">press</span>
<span class="n">thermo_modify</span> <span class="n">temp</span> <span class="n">effTemp</span>
</pre></div>
</div>
<p>The value of the kinetic energy will be 0.0 for atoms (nuclei or
electrons) not in the specified compute group.</p>
<p><strong>Output info:</strong></p>

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@ -169,11 +169,11 @@ the <a class="reference internal" href="compute_temp_eff.html"><span class="doc"
printed with thermodynamic output by using the
<a class="reference internal" href="thermo_modify.html"><span class="doc">thermo_modify</span></a> command, as shown in the following
example:</p>
<pre class="literal-block">
compute effTemp all temp/eff
thermo_style custom step etotal pe ke temp press
thermo_modify temp effTemp
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">effTemp</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">eff</span>
<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">etotal</span> <span class="n">pe</span> <span class="n">ke</span> <span class="n">temp</span> <span class="n">press</span>
<span class="n">thermo_modify</span> <span class="n">temp</span> <span class="n">effTemp</span>
</pre></div>
</div>
<p>See <a class="reference internal" href="compute_temp_eff.html"><span class="doc">compute temp/eff</span></a>.</p>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global scalar (the KE). This value can be

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@ -128,9 +128,9 @@
<span id="index-0"></span><h1>compute_modify command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
compute_modify compute-ID keyword value ...
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute_modify</span> <span class="n">compute</span><span class="o">-</span><span class="n">ID</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
</pre></div>
</div>
<ul class="simple">
<li>compute-ID = ID of the compute to modify</li>
<li>one or more keyword/value pairs may be listed</li>
@ -145,10 +145,10 @@ compute_modify compute-ID keyword value ...
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
compute_modify myTemp extra 0
compute_modify newtemp dynamic yes extra 600
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute_modify</span> <span class="n">myTemp</span> <span class="n">extra</span> <span class="mi">0</span>
<span class="n">compute_modify</span> <span class="n">newtemp</span> <span class="n">dynamic</span> <span class="n">yes</span> <span class="n">extra</span> <span class="mi">600</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

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@ -185,11 +185,11 @@ command.</p>
<p>As an example of per-atom potential energy compared to total potential
energy, these lines in an input script should yield the same result
in the last 2 columns of thermo output:</p>
<pre class="literal-block">
compute peratom all pe/atom
compute pe all reduce sum c_peratom
thermo_style custom step temp etotal press pe c_pe
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">peratom</span> <span class="nb">all</span> <span class="n">pe</span><span class="o">/</span><span class="n">atom</span>
<span class="n">compute</span> <span class="n">pe</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">sum</span> <span class="n">c_peratom</span>
<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">etotal</span> <span class="n">press</span> <span class="n">pe</span> <span class="n">c_pe</span>
</pre></div>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The per-atom energy does not any Lennard-Jones tail corrections

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@ -136,25 +136,25 @@
<li>property/atom = style name of this compute command</li>
<li>input = one or more atom attributes</li>
</ul>
<pre class="literal-block">
possible attributes = id, mol, proc, type, mass,
x, y, z, xs, ys, zs, xu, yu, zu, ix, iy, iz,
vx, vy, vz, fx, fy, fz,
q, mux, muy, muz, mu,
radius, diameter, omegax, omegay, omegaz,
angmomx, angmomy, angmomz,
shapex,shapey, shapez,
quatw, quati, quatj, quatk, tqx, tqy, tqz,
end1x, end1y, end1z, end2x, end2y, end2z,
corner1x, corner1y, corner1z,
corner2x, corner2y, corner2z,
corner3x, corner3y, corner3z,
nbonds,
vfrac, s0,
spin, eradius, ervel, erforce,
rho, drho, e, de, cv,
i_name, d_name
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">possible</span> <span class="n">attributes</span> <span class="o">=</span> <span class="nb">id</span><span class="p">,</span> <span class="n">mol</span><span class="p">,</span> <span class="n">proc</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="n">mass</span><span class="p">,</span>
<span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">z</span><span class="p">,</span> <span class="n">xs</span><span class="p">,</span> <span class="n">ys</span><span class="p">,</span> <span class="n">zs</span><span class="p">,</span> <span class="n">xu</span><span class="p">,</span> <span class="n">yu</span><span class="p">,</span> <span class="n">zu</span><span class="p">,</span> <span class="n">ix</span><span class="p">,</span> <span class="n">iy</span><span class="p">,</span> <span class="n">iz</span><span class="p">,</span>
<span class="n">vx</span><span class="p">,</span> <span class="n">vy</span><span class="p">,</span> <span class="n">vz</span><span class="p">,</span> <span class="n">fx</span><span class="p">,</span> <span class="n">fy</span><span class="p">,</span> <span class="n">fz</span><span class="p">,</span>
<span class="n">q</span><span class="p">,</span> <span class="n">mux</span><span class="p">,</span> <span class="n">muy</span><span class="p">,</span> <span class="n">muz</span><span class="p">,</span> <span class="n">mu</span><span class="p">,</span>
<span class="n">radius</span><span class="p">,</span> <span class="n">diameter</span><span class="p">,</span> <span class="n">omegax</span><span class="p">,</span> <span class="n">omegay</span><span class="p">,</span> <span class="n">omegaz</span><span class="p">,</span>
<span class="n">angmomx</span><span class="p">,</span> <span class="n">angmomy</span><span class="p">,</span> <span class="n">angmomz</span><span class="p">,</span>
<span class="n">shapex</span><span class="p">,</span><span class="n">shapey</span><span class="p">,</span> <span class="n">shapez</span><span class="p">,</span>
<span class="n">quatw</span><span class="p">,</span> <span class="n">quati</span><span class="p">,</span> <span class="n">quatj</span><span class="p">,</span> <span class="n">quatk</span><span class="p">,</span> <span class="n">tqx</span><span class="p">,</span> <span class="n">tqy</span><span class="p">,</span> <span class="n">tqz</span><span class="p">,</span>
<span class="n">end1x</span><span class="p">,</span> <span class="n">end1y</span><span class="p">,</span> <span class="n">end1z</span><span class="p">,</span> <span class="n">end2x</span><span class="p">,</span> <span class="n">end2y</span><span class="p">,</span> <span class="n">end2z</span><span class="p">,</span>
<span class="n">corner1x</span><span class="p">,</span> <span class="n">corner1y</span><span class="p">,</span> <span class="n">corner1z</span><span class="p">,</span>
<span class="n">corner2x</span><span class="p">,</span> <span class="n">corner2y</span><span class="p">,</span> <span class="n">corner2z</span><span class="p">,</span>
<span class="n">corner3x</span><span class="p">,</span> <span class="n">corner3y</span><span class="p">,</span> <span class="n">corner3z</span><span class="p">,</span>
<span class="n">nbonds</span><span class="p">,</span>
<span class="n">vfrac</span><span class="p">,</span> <span class="n">s0</span><span class="p">,</span>
<span class="n">spin</span><span class="p">,</span> <span class="n">eradius</span><span class="p">,</span> <span class="n">ervel</span><span class="p">,</span> <span class="n">erforce</span><span class="p">,</span>
<span class="n">rho</span><span class="p">,</span> <span class="n">drho</span><span class="p">,</span> <span class="n">e</span><span class="p">,</span> <span class="n">de</span><span class="p">,</span> <span class="n">cv</span><span class="p">,</span>
<span class="n">i_name</span><span class="p">,</span> <span class="n">d_name</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="nb">id</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">ID</span>
<span class="n">mol</span> <span class="o">=</span> <span class="n">molecule</span> <span class="n">ID</span>
<span class="n">proc</span> <span class="o">=</span> <span class="n">ID</span> <span class="n">of</span> <span class="n">processor</span> <span class="n">that</span> <span class="n">owns</span> <span class="n">atom</span>

12
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@ -192,12 +192,12 @@ will be in unitless reduced units (0-1).</p>
<p>The simplest way to output the results of the compute property/chunk
calculation to a file is to use the <a class="reference internal" href="fix_ave_time.html"><span class="doc">fix ave/time</span></a>
command, for example:</p>
<pre class="literal-block">
compute cc1 all chunk/atom molecule
compute myChunk1 all property/chunk cc1 count
compute myChunk2 all com/chunk cc1
fix 1 all ave/time 100 1 100 c_myChunk1 c_myChunk2[*] file tmp.out mode vector
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cc1</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">molecule</span>
<span class="n">compute</span> <span class="n">myChunk1</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span> <span class="n">count</span>
<span class="n">compute</span> <span class="n">myChunk2</span> <span class="nb">all</span> <span class="n">com</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myChunk1</span> <span class="n">c_myChunk2</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span> <span class="n">mode</span> <span class="n">vector</span>
</pre></div>
</div>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global vector or global array depending on
the number of input values. The length of the vector or number of

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@ -148,14 +148,14 @@
<li>one or more inputs can be listed</li>
<li>input = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name</li>
</ul>
<pre class="literal-block">
x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
c_ID = per-atom or local vector calculated by a compute with ID
c_ID[I] = Ith column of per-atom or local array calculated by a compute with ID, I can include wildcard (see below)
f_ID = per-atom or local vector calculated by a fix with ID
f_ID[I] = Ith column of per-atom or local array calculated by a fix with ID, I can include wildcard (see below)
v_name = per-atom vector calculated by an atom-style variable with name
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">,</span><span class="n">z</span><span class="p">,</span><span class="n">vx</span><span class="p">,</span><span class="n">vy</span><span class="p">,</span><span class="n">vz</span><span class="p">,</span><span class="n">fx</span><span class="p">,</span><span class="n">fy</span><span class="p">,</span><span class="n">fz</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">attribute</span> <span class="p">(</span><span class="n">position</span><span class="p">,</span> <span class="n">velocity</span><span class="p">,</span> <span class="n">force</span> <span class="n">component</span><span class="p">)</span>
<span class="n">c_ID</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="ow">or</span> <span class="n">local</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
<span class="n">c_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="ow">or</span> <span class="n">local</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
<span class="n">f_ID</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="ow">or</span> <span class="n">local</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
<span class="n">f_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="ow">or</span> <span class="n">local</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
<span class="n">v_name</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">an</span> <span class="n">atom</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
</pre></div>
</div>
<ul class="simple">
<li>zero or more keyword/args pairs may be appended</li>
<li>keyword = <em>replace</em></li>
@ -168,13 +168,13 @@ v_name = per-atom vector calculated by an atom-style variable with name
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
compute 1 all reduce sum c_force
compute 1 all reduce/region subbox sum c_force
compute 2 all reduce min c_press[2] f_ave v_myKE
compute 2 all reduce min c_press[*] f_ave v_myKE
compute 3 fluid reduce max c_index[1] c_index[2] c_dist replace 1 3 replace 2 3
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">sum</span> <span class="n">c_force</span>
<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">reduce</span><span class="o">/</span><span class="n">region</span> <span class="n">subbox</span> <span class="nb">sum</span> <span class="n">c_force</span>
<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">min</span> <span class="n">c_press</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">f_ave</span> <span class="n">v_myKE</span>
<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">min</span> <span class="n">c_press</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">f_ave</span> <span class="n">v_myKE</span>
<span class="n">compute</span> <span class="mi">3</span> <span class="n">fluid</span> <span class="n">reduce</span> <span class="nb">max</span> <span class="n">c_index</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_index</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_dist</span> <span class="n">replace</span> <span class="mi">1</span> <span class="mi">3</span> <span class="n">replace</span> <span class="mi">2</span> <span class="mi">3</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -211,7 +211,7 @@ component) or can be the result of a <a class="reference internal" href="compute
<a class="reference internal" href="variable.html"><span class="doc">variable</span></a>.</p>
<p>Note that for values from a compute or fix, the bracketed index I can
be specified using a wildcard asterisk with the index to effectively
specify multiple values. This takes the form &#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or
specify multiple values. This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or
&#8220;m*n&#8221;. If N = the size of the vector (for <em>mode</em> = scalar) or the
number of columns in the array (for <em>mode</em> = vector), then an asterisk
with no numeric values means all indices from 1 to N. A leading
@ -222,18 +222,18 @@ means all indices from m to n (inclusive).</p>
had been listed one by one. E.g. these 2 compute reduce commands are
equivalent, since the <a class="reference internal" href="compute_stress_atom.html"><span class="doc">compute stress/atom</span></a>
command creates a per-atom array with 6 columns:</p>
<pre class="literal-block">
compute myPress all stress/atom NULL
compute 2 all reduce min myPress[*]
compute 2 all reduce min myPress[1] myPress[2] myPress[3] &amp;
myPress[4] myPress[5] myPress[6]
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">myPress</span> <span class="nb">all</span> <span class="n">stress</span><span class="o">/</span><span class="n">atom</span> <span class="n">NULL</span>
<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">min</span> <span class="n">myPress</span><span class="p">[</span><span class="o">*</span><span class="p">]</span>
<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">min</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">&amp;</span>
<span class="n">myPress</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span>
</pre></div>
</div>
<hr class="docutils" />
<p>The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are
self-explanatory. Note that other atom attributes can be used as
inputs to this fix by using the <a class="reference internal" href="compute_property_atom.html"><span class="doc">compute property/atom</span></a> command and then specifying
an input value from that compute.</p>
<p>If a value begins with &#8220;c_&#8221;, a compute ID must follow which has been
<p>If a value begins with &#8220;<a href="#id1"><span class="problematic" id="id2">c_</span></a>&#8221;, a compute ID must follow which has been
previously defined in the input script. Computes can generate
per-atom or local quantities. See the individual
<a class="reference internal" href="compute.html"><span class="doc">compute</span></a> doc page for details. If no bracketed integer
@ -243,7 +243,7 @@ by the compute is used. Users can also write code for their own
compute styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>. See the
discussion above for how I can be specified with a wildcard asterisk
to effectively specify multiple values.</p>
<p>If a value begins with &#8220;f_&#8221;, a fix ID must follow which has been
<p>If a value begins with &#8220;<a href="#id3"><span class="problematic" id="id4">f_</span></a>&#8221;, a fix ID must follow which has been
previously defined in the input script. Fixes can generate per-atom
or local quantities. See the individual <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> doc page for
details. Note that some fixes only produce their values on certain
@ -254,7 +254,7 @@ integer is appended, the Ith column of the array calculated by the fix
is used. Users can also write code for their own fix style and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>. See the discussion above for how
I can be specified with a wildcard asterisk to effectively specify
multiple values.</p>
<p>If a value begins with &#8220;v_&#8221;, a variable name must follow which has
<p>If a value begins with &#8220;<a href="#id5"><span class="problematic" id="id6">v_</span></a>&#8221;, a variable name must follow which has
been previously defined in the input script. It must be an
<a class="reference internal" href="variable.html"><span class="doc">atom-style variable</span></a>. Atom-style variables can
reference thermodynamic keywords and various per-atom attributes, or
@ -271,12 +271,12 @@ Then, instead of performing a min/max on the <em>vec1</em> input vector, the
stored index is used to select the Nth element of the <em>vec1</em> vector.</p>
<p>Thus, for example, if you wish to use this compute to find the bond
with maximum stretch, you can do it as follows:</p>
<pre class="literal-block">
compute 1 all property/local batom1 batom2
compute 2 all bond/local dist
compute 3 all reduce max c_1[1] c_1[2] c_2 replace 1 3 replace 2 3
thermo_style custom step temp c_3[1] c_3[2] c_3[3]
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">local</span> <span class="n">batom1</span> <span class="n">batom2</span>
<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">bond</span><span class="o">/</span><span class="n">local</span> <span class="n">dist</span>
<span class="n">compute</span> <span class="mi">3</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">max</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_2</span> <span class="n">replace</span> <span class="mi">1</span> <span class="mi">3</span> <span class="n">replace</span> <span class="mi">2</span> <span class="mi">3</span>
<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">c_3</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_3</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_3</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span>
</pre></div>
</div>
<p>The first two input values in the compute reduce command are vectors
with the IDs of the 2 atoms in each bond, using the <a class="reference internal" href="compute_property_local.html"><span class="doc">compute property/local</span></a> command. The last input
value is bond distance, using the <a class="reference internal" href="compute_bond_local.html"><span class="doc">compute bond/local</span></a> command. Instead of taking the

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@ -202,10 +202,10 @@ there will be no consistent ordering of the entries within the local
vector or array from one timestep to the next.</p>
<p>Here is an example of how to use this compute to dump rigid body info
to a file:</p>
<pre class="literal-block">
compute 1 all rigid/local myRigid mol x y z fx fy fz
dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_1[5] c_1[6] c_1[7]
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">rigid</span><span class="o">/</span><span class="n">local</span> <span class="n">myRigid</span> <span class="n">mol</span> <span class="n">x</span> <span class="n">y</span> <span class="n">z</span> <span class="n">fx</span> <span class="n">fy</span> <span class="n">fz</span>
<span class="n">dump</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">local</span> <span class="mi">1000</span> <span class="n">tmp</span><span class="o">.</span><span class="n">dump</span> <span class="n">index</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">7</span><span class="p">]</span>
</pre></div>
</div>
<hr class="docutils" />
<p>This section explains the rigid body attributes that can be specified.</p>
<p>The <em>id</em> attribute is the atomID of the atom which owns the rigid body, which is

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@ -140,10 +140,10 @@
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
compute oxygen_c-s all temp/cs O_core O_shell
compute core_shells all temp/cs cores shells
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">oxygen_c</span><span class="o">-</span><span class="n">s</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">cs</span> <span class="n">O_core</span> <span class="n">O_shell</span>
<span class="n">compute</span> <span class="n">core_shells</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">cs</span> <span class="n">cores</span> <span class="n">shells</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>

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@ -170,11 +170,11 @@ reported by LAMMPS in the thermodynamic quantities reported via the
<a class="reference internal" href="thermo_modify.html"><span class="doc">thermo_modify</span></a> command, as shown in the following
example:</p>
</div>
<pre class="literal-block">
compute effTemp all temp/eff
thermo_style custom step etotal pe ke temp press
thermo_modify temp effTemp
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">effTemp</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">eff</span>
<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">etotal</span> <span class="n">pe</span> <span class="n">ke</span> <span class="n">temp</span> <span class="n">press</span>
<span class="n">thermo_modify</span> <span class="n">temp</span> <span class="n">effTemp</span>
</pre></div>
</div>
<p>A 6-component kinetic energy tensor is also calculated by this compute
for use in the computation of a pressure tensor. The formula for the
components of the tensor is the same as the above formula, except that

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@ -154,10 +154,10 @@ pair style args = atype v_name1 v_name2
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
compute 1 all ti lj/cut 1 v_lj v_dlj coul/long 2 v_c v_dc kspace 1 v_ks v_dks
compute 1 all ti lj/cut 1*3 v_lj v_dlj coul/long * v_c v_dc kspace * v_ks v_dks
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ti</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mi">1</span> <span class="n">v_lj</span> <span class="n">v_dlj</span> <span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="mi">2</span> <span class="n">v_c</span> <span class="n">v_dc</span> <span class="n">kspace</span> <span class="mi">1</span> <span class="n">v_ks</span> <span class="n">v_dks</span>
<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ti</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mi">1</span><span class="o">*</span><span class="mi">3</span> <span class="n">v_lj</span> <span class="n">v_dlj</span> <span class="n">coul</span><span class="o">/</span><span class="n">long</span> <span class="o">*</span> <span class="n">v_c</span> <span class="n">v_dc</span> <span class="n">kspace</span> <span class="o">*</span> <span class="n">v_ks</span> <span class="n">v_dks</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -192,7 +192,7 @@ with respect to <em>lambda</em>.</p>
numeric values can be used, as in the 1st example above. Or a
wildcard asterisk can be used in place of or in conjunction with the
<em>atype</em> argument to select multiple atom types. This takes the form
&#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or &#8220;m*n&#8221;. If N = the number of atom types, then
&#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or &#8220;m*n&#8221;. If N = the number of atom types, then
an asterisk with no numeric values means all types from 1 to N. A
leading asterisk means all types from 1 to n (inclusive). A trailing
asterisk means all types from n to N (inclusive). A middle asterisk

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@ -158,14 +158,14 @@ or <em>face_threshold</em> or <em>neighbors</em> or <em>peratom</em></li>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
compute 1 all voronoi/atom
compute 2 precipitate voronoi/atom surface matrix
compute 3b precipitate voronoi/atom radius v_r
compute 4 solute voronoi/atom only_group
compute 5 defects voronoi/atom occupation
compute 6 all voronoi/atom neighbors yes
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span>
<span class="n">compute</span> <span class="mi">2</span> <span class="n">precipitate</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span> <span class="n">surface</span> <span class="n">matrix</span>
<span class="n">compute</span> <span class="mi">3</span><span class="n">b</span> <span class="n">precipitate</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span> <span class="n">radius</span> <span class="n">v_r</span>
<span class="n">compute</span> <span class="mi">4</span> <span class="n">solute</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span> <span class="n">only_group</span>
<span class="n">compute</span> <span class="mi">5</span> <span class="n">defects</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span> <span class="n">occupation</span>
<span class="n">compute</span> <span class="mi">6</span> <span class="nb">all</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span> <span class="n">neighbors</span> <span class="n">yes</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -199,11 +199,11 @@ can be obtained by running a &#8220;reduce sum&#8221; compute on c_2[3]</p>
<p>If the <em>radius</em> keyword is specified with an atom style variable as
the argument, a poly-disperse Voronoi tessellation is
performed. Examples for radius variables are</p>
<pre class="literal-block">
variable r1 atom (type==1)*0.1+(type==2)*0.4
compute radius all property/atom radius
variable r2 atom c_radius
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">r1</span> <span class="n">atom</span> <span class="p">(</span><span class="nb">type</span><span class="o">==</span><span class="mi">1</span><span class="p">)</span><span class="o">*</span><span class="mf">0.1</span><span class="o">+</span><span class="p">(</span><span class="nb">type</span><span class="o">==</span><span class="mi">2</span><span class="p">)</span><span class="o">*</span><span class="mf">0.4</span>
<span class="n">compute</span> <span class="n">radius</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">atom</span> <span class="n">radius</span>
<span class="n">variable</span> <span class="n">r2</span> <span class="n">atom</span> <span class="n">c_radius</span>
</pre></div>
</div>
<p>Here v_r1 specifies a per-type radius of 0.1 units for type 1 atoms
and 0.4 units for type 2 atoms, and v_r2 accesses the radius property
present in atom_style sphere for granular models.</p>
@ -247,10 +247,10 @@ uses local values from a compute as input. See <a class="reference internal" hr
options. More specifically, the array can be accessed by a
<a class="reference internal" href="dump.html"><span class="doc">dump local</span></a> command to write a file containing
all the Voronoi neighbors in a system:</p>
<pre class="literal-block">
compute 6 all voronoi/atom neighbors yes
dump d2 all local 1 dump.neighbors index c_6[1] c_6[2] c_6[3]
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">6</span> <span class="nb">all</span> <span class="n">voronoi</span><span class="o">/</span><span class="n">atom</span> <span class="n">neighbors</span> <span class="n">yes</span>
<span class="n">dump</span> <span class="n">d2</span> <span class="nb">all</span> <span class="n">local</span> <span class="mi">1</span> <span class="n">dump</span><span class="o">.</span><span class="n">neighbors</span> <span class="n">index</span> <span class="n">c_6</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_6</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_6</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span>
</pre></div>
</div>
<p>If the <em>face_threshold</em> keyword is used, then only faces
with areas greater than the threshold are stored.</p>
<hr class="docutils" />

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@ -128,9 +128,9 @@
<span id="index-0"></span><h1>delete_bonds command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
delete_bonds group-ID style arg keyword ...
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">delete_bonds</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">style</span> <span class="n">arg</span> <span class="n">keyword</span> <span class="o">...</span>
</pre></div>
</div>
<ul>
<li><p class="first">group-ID = group ID</p>
</li>
@ -157,12 +157,12 @@ delete_bonds group-ID style arg keyword ...
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
delete_bonds frozen multi remove
delete_bonds all atom 4 special
delete_bonds all bond 0*3 special
delete_bonds all stats
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">delete_bonds</span> <span class="n">frozen</span> <span class="n">multi</span> <span class="n">remove</span>
<span class="n">delete_bonds</span> <span class="nb">all</span> <span class="n">atom</span> <span class="mi">4</span> <span class="n">special</span>
<span class="n">delete_bonds</span> <span class="nb">all</span> <span class="n">bond</span> <span class="mi">0</span><span class="o">*</span><span class="mi">3</span> <span class="n">special</span>
<span class="n">delete_bonds</span> <span class="nb">all</span> <span class="n">stats</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -183,7 +183,7 @@ be an integer from 0 to N, where N is the number of relevant types
(atom types, bond types, etc). A value of 0 is only relevant for
style <em>bond</em>; see details below. In all cases, a wildcard asterisk
can be used in place of or in conjunction with the <em>type</em> argument to
specify a range of types. This takes the form &#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or
specify a range of types. This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or
&#8220;m*n&#8221;. If N = the number of types, then an asterisk with no numeric
values means all types from 0 to N. A leading asterisk means all
types from 0 to n (inclusive). A trailing asterisk means all types

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@ -131,9 +131,9 @@
<h1>dihedral_style table/omp command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
dihedral_style table style Ntable
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">table</span> <span class="n">style</span> <span class="n">Ntable</span>
</pre></div>
</div>
<ul class="simple">
<li>style = <em>linear</em> or <em>spline</em> = method of interpolation</li>
<li>Ntable = size of the internal lookup table</li>
@ -141,12 +141,12 @@ dihedral_style table style Ntable
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
dihedral_style table spline 400
dihedral_style table linear 1000
dihedral_coeff 1 file.table DIH_TABLE1
dihedral_coeff 2 file.table DIH_TABLE2
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">table</span> <span class="n">spline</span> <span class="mi">400</span>
<span class="n">dihedral_style</span> <span class="n">table</span> <span class="n">linear</span> <span class="mi">1000</span>
<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="n">file</span><span class="o">.</span><span class="n">table</span> <span class="n">DIH_TABLE1</span>
<span class="n">dihedral_coeff</span> <span class="mi">2</span> <span class="n">file</span><span class="o">.</span><span class="n">table</span> <span class="n">DIH_TABLE2</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -185,23 +185,23 @@ or blank lines.</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Table of the potential and its negative derivative</span>
</pre></div>
</div>
<pre class="literal-block">
DIH_TABLE1 (keyword is the first text on line)
N 30 DEGREES (N, NOF, DEGREES, RADIANS, CHECKU/F)
(blank line)
1 -168.0 -1.40351172223 0.0423346818422
2 -156.0 -1.70447981034 0.00811786522531
3 -144.0 -1.62956100432 -0.0184129719987
...
30 180.0 -0.707106781187 0.0719306095245
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">DIH_TABLE1</span> <span class="p">(</span><span class="n">keyword</span> <span class="ow">is</span> <span class="n">the</span> <span class="n">first</span> <span class="n">text</span> <span class="n">on</span> <span class="n">line</span><span class="p">)</span>
<span class="n">N</span> <span class="mi">30</span> <span class="n">DEGREES</span> <span class="p">(</span><span class="n">N</span><span class="p">,</span> <span class="n">NOF</span><span class="p">,</span> <span class="n">DEGREES</span><span class="p">,</span> <span class="n">RADIANS</span><span class="p">,</span> <span class="n">CHECKU</span><span class="o">/</span><span class="n">F</span><span class="p">)</span>
<span class="p">(</span><span class="n">blank</span> <span class="n">line</span><span class="p">)</span>
<span class="mi">1</span> <span class="o">-</span><span class="mf">168.0</span> <span class="o">-</span><span class="mf">1.40351172223</span> <span class="mf">0.0423346818422</span>
<span class="mi">2</span> <span class="o">-</span><span class="mf">156.0</span> <span class="o">-</span><span class="mf">1.70447981034</span> <span class="mf">0.00811786522531</span>
<span class="mi">3</span> <span class="o">-</span><span class="mf">144.0</span> <span class="o">-</span><span class="mf">1.62956100432</span> <span class="o">-</span><span class="mf">0.0184129719987</span>
<span class="o">...</span>
<span class="mi">30</span> <span class="mf">180.0</span> <span class="o">-</span><span class="mf">0.707106781187</span> <span class="mf">0.0719306095245</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Example 2: table of the potential. Forces omitted</span>
</pre></div>
</div>
<pre class="literal-block">
DIH_TABLE2
N 30 NOF CHECKU testU.dat CHECKF testF.dat
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">DIH_TABLE2</span>
<span class="n">N</span> <span class="mi">30</span> <span class="n">NOF</span> <span class="n">CHECKU</span> <span class="n">testU</span><span class="o">.</span><span class="n">dat</span> <span class="n">CHECKF</span> <span class="n">testF</span><span class="o">.</span><span class="n">dat</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="mi">1</span> <span class="o">-</span><span class="mf">168.0</span> <span class="o">-</span><span class="mf">1.40351172223</span>
<span class="mi">2</span> <span class="o">-</span><span class="mf">156.0</span> <span class="o">-</span><span class="mf">1.70447981034</span>
<span class="mi">3</span> <span class="o">-</span><span class="mf">144.0</span> <span class="o">-</span><span class="mf">1.62956100432</span>

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@ -239,19 +239,19 @@ i_name = per-atom integer vector with name, managed by fix property/atom
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
dump myDump all atom 100 dump.atom
dump myDump all atom/mpiio 100 dump.atom.mpiio
dump myDump all atom/gz 100 dump.atom.gz
dump 2 subgroup atom 50 dump.run.bin
dump 2 subgroup atom 50 dump.run.mpiio.bin
dump 4a all custom 100 dump.myforce.* id type x y vx fx
dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
dump 4b flow custom 100 dump.%.myforce id type c_myF[*] v_ke
dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz
dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress[2]
dump 1 all xtc 1000 file.xtc
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dump</span> <span class="n">myDump</span> <span class="nb">all</span> <span class="n">atom</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">.</span><span class="n">atom</span>
<span class="n">dump</span> <span class="n">myDump</span> <span class="nb">all</span> <span class="n">atom</span><span class="o">/</span><span class="n">mpiio</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">.</span><span class="n">atom</span><span class="o">.</span><span class="n">mpiio</span>
<span class="n">dump</span> <span class="n">myDump</span> <span class="nb">all</span> <span class="n">atom</span><span class="o">/</span><span class="n">gz</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">.</span><span class="n">atom</span><span class="o">.</span><span class="n">gz</span>
<span class="n">dump</span> <span class="mi">2</span> <span class="n">subgroup</span> <span class="n">atom</span> <span class="mi">50</span> <span class="n">dump</span><span class="o">.</span><span class="n">run</span><span class="o">.</span><span class="n">bin</span>
<span class="n">dump</span> <span class="mi">2</span> <span class="n">subgroup</span> <span class="n">atom</span> <span class="mi">50</span> <span class="n">dump</span><span class="o">.</span><span class="n">run</span><span class="o">.</span><span class="n">mpiio</span><span class="o">.</span><span class="n">bin</span>
<span class="n">dump</span> <span class="mi">4</span><span class="n">a</span> <span class="nb">all</span> <span class="n">custom</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">.</span><span class="n">myforce</span><span class="o">.*</span> <span class="nb">id</span> <span class="nb">type</span> <span class="n">x</span> <span class="n">y</span> <span class="n">vx</span> <span class="n">fx</span>
<span class="n">dump</span> <span class="mi">4</span><span class="n">b</span> <span class="n">flow</span> <span class="n">custom</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">.%.</span><span class="n">myforce</span> <span class="nb">id</span> <span class="nb">type</span> <span class="n">c_myF</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">v_ke</span>
<span class="n">dump</span> <span class="mi">4</span><span class="n">b</span> <span class="n">flow</span> <span class="n">custom</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">.%.</span><span class="n">myforce</span> <span class="nb">id</span> <span class="nb">type</span> <span class="n">c_myF</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">v_ke</span>
<span class="n">dump</span> <span class="mi">2</span> <span class="n">inner</span> <span class="n">cfg</span> <span class="mi">10</span> <span class="n">dump</span><span class="o">.</span><span class="n">snap</span><span class="o">.*.</span><span class="n">cfg</span> <span class="n">mass</span> <span class="nb">type</span> <span class="n">xs</span> <span class="n">ys</span> <span class="n">zs</span> <span class="n">vx</span> <span class="n">vy</span> <span class="n">vz</span>
<span class="n">dump</span> <span class="n">snap</span> <span class="nb">all</span> <span class="n">cfg</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">.</span><span class="n">config</span><span class="o">.*.</span><span class="n">cfg</span> <span class="n">mass</span> <span class="nb">type</span> <span class="n">xs</span> <span class="n">ys</span> <span class="n">zs</span> <span class="nb">id</span> <span class="nb">type</span> <span class="n">c_Stress</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
<span class="n">dump</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">xtc</span> <span class="mi">1000</span> <span class="n">file</span><span class="o">.</span><span class="n">xtc</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -347,12 +347,12 @@ or m = shrink wrapped with a minimum value. See the
bounding box which encloses the triclinic simulation box is output,
along with the 3 tilt factors (xy, xz, yz) of the triclinic box,
formatted as follows:</p>
<pre class="literal-block">
ITEM: BOX BOUNDS xy xz yz xx yy zz
xlo_bound xhi_bound xy
ylo_bound yhi_bound xz
zlo_bound zhi_bound yz
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">ITEM</span><span class="p">:</span> <span class="n">BOX</span> <span class="n">BOUNDS</span> <span class="n">xy</span> <span class="n">xz</span> <span class="n">yz</span> <span class="n">xx</span> <span class="n">yy</span> <span class="n">zz</span>
<span class="n">xlo_bound</span> <span class="n">xhi_bound</span> <span class="n">xy</span>
<span class="n">ylo_bound</span> <span class="n">yhi_bound</span> <span class="n">xz</span>
<span class="n">zlo_bound</span> <span class="n">zhi_bound</span> <span class="n">yz</span>
</pre></div>
</div>
<p>The presence of the text &#8220;xy xz yz&#8221; in the ITEM line indicates that
the 3 tilt factors will be included on each of the 3 following lines.
This bounding box is convenient for many visualization programs. The
@ -541,7 +541,7 @@ styles.</p>
reference values from a compute or fix, like the <em>custom</em>, <em>cfg</em>, or
<em>local</em> styles, the bracketed index I can be specified using a
wildcard asterisk with the index to effectively specify multiple
values. This takes the form &#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or &#8220;m*n&#8221;. If N = the
values. This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or &#8220;m*n&#8221;. If N = the
size of the vector (for <em>mode</em> = scalar) or the number of columns in
the array (for <em>mode</em> = vector), then an asterisk with no numeric
values means all indices from 1 to N. A leading asterisk means all
@ -552,12 +552,12 @@ from m to n (inclusive).</p>
had been listed one by one. E.g. these 2 dump commands are
equivalent, since the <a class="reference internal" href="compute_stress_atom.html"><span class="doc">compute stress/atom</span></a>
command creates a per-atom array with 6 columns:</p>
<pre class="literal-block">
compute myPress all stress/atom NULL
dump 2 all custom 100 tmp.dump id myPress[*]
dump 2 all custom 100 tmp.dump id myPress[1] myPress[2] myPress[3] &amp;
myPress[4] myPress[5] myPress[6]
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">myPress</span> <span class="nb">all</span> <span class="n">stress</span><span class="o">/</span><span class="n">atom</span> <span class="n">NULL</span>
<span class="n">dump</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">custom</span> <span class="mi">100</span> <span class="n">tmp</span><span class="o">.</span><span class="n">dump</span> <span class="nb">id</span> <span class="n">myPress</span><span class="p">[</span><span class="o">*</span><span class="p">]</span>
<span class="n">dump</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">custom</span> <span class="mi">100</span> <span class="n">tmp</span><span class="o">.</span><span class="n">dump</span> <span class="nb">id</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">&amp;</span>
<span class="n">myPress</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span> <span class="n">myPress</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span>
</pre></div>
</div>
<hr class="docutils" />
<p>This section explains the local attributes that can be specified as
part of the <em>local</em> style.</p>
@ -598,11 +598,11 @@ be specified with a wildcard asterisk to effectively specify multiple
values.</p>
<p>Here is an example of how to dump bond info for a system, including
the distance and energy of each bond:</p>
<pre class="literal-block">
compute 1 all property/local batom1 batom2 btype
compute 2 all bond/local dist eng
dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2]
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">local</span> <span class="n">batom1</span> <span class="n">batom2</span> <span class="n">btype</span>
<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">bond</span><span class="o">/</span><span class="n">local</span> <span class="n">dist</span> <span class="n">eng</span>
<span class="n">dump</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">local</span> <span class="mi">1000</span> <span class="n">tmp</span><span class="o">.</span><span class="n">dump</span> <span class="n">index</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">c_2</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_2</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
</pre></div>
</div>
<hr class="docutils" />
<p>This section explains the atom attributes that can be specified as
part of the <em>custom</em> and <em>cfg</em> styles.</p>

12
doc/html/dump_custom_vtk.html
View File

@ -182,15 +182,15 @@ v_name = per-atom vector calculated by an atom-style variable with name
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
dump dmpvtk all custom/vtk 100 dump*.myforce.vtk id type vx fx
dump dmpvtp flow custom/vtk 100 dump*.%.displace.vtp id type c_myD[1] c_myD[2] c_myD[3] v_ke
dump e_data all custom/vtk 100 dump*.vtu id type spin eradius fx fy fz eforce
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dump</span> <span class="n">dmpvtk</span> <span class="nb">all</span> <span class="n">custom</span><span class="o">/</span><span class="n">vtk</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">*.</span><span class="n">myforce</span><span class="o">.</span><span class="n">vtk</span> <span class="nb">id</span> <span class="nb">type</span> <span class="n">vx</span> <span class="n">fx</span>
<span class="n">dump</span> <span class="n">dmpvtp</span> <span class="n">flow</span> <span class="n">custom</span><span class="o">/</span><span class="n">vtk</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">*.%.</span><span class="n">displace</span><span class="o">.</span><span class="n">vtp</span> <span class="nb">id</span> <span class="nb">type</span> <span class="n">c_myD</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_myD</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_myD</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">v_ke</span>
<span class="n">dump</span> <span class="n">e_data</span> <span class="nb">all</span> <span class="n">custom</span><span class="o">/</span><span class="n">vtk</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">*.</span><span class="n">vtu</span> <span class="nb">id</span> <span class="nb">type</span> <span class="n">spin</span> <span class="n">eradius</span> <span class="n">fx</span> <span class="n">fy</span> <span class="n">fz</span> <span class="n">eforce</span>
</pre></div>
</div>
<p>The style <em>custom/vtk</em> is similar to the <a class="reference internal" href="dump.html"><span class="doc">custom</span></a> style but
uses the VTK library to write data to VTK simple legacy or XML format
depending on the filename extension specified. This can be either
<em>*.vtk</em> for the legacy format or <em>*.vtp</em> and <em>*.vtu</em>, respectively,
<a href="#id1"><span class="problematic" id="id2">**</span></a>.vtk* for the legacy format or <a href="#id3"><span class="problematic" id="id4">**</span></a>.vtp* and <a href="#id5"><span class="problematic" id="id6">**</span></a>.vtu*, respectively,
for the XML format; see the <a class="reference external" href="http://www.vtk.org/VTK/img/file-formats.pdf">VTK homepage</a> for a detailed
description of these formats. Since this naming convention conflicts
with the way binary output is usually specified (see below),

70
doc/html/dump_modify.html
View File

@ -128,9 +128,9 @@
<span id="index-0"></span><h1>dump_modify command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
dump_modify dump-ID keyword values ...
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dump_modify</span> <span class="n">dump</span><span class="o">-</span><span class="n">ID</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
</pre></div>
</div>
<ul class="simple">
<li>dump-ID = ID of dump to modify</li>
<li>one or more keyword/value pairs may be appended</li>
@ -228,16 +228,16 @@ dump_modify dump-ID keyword values ...
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
dump_modify 1 format line &quot;%d %d %20.15g %g %g&quot; scale yes
dump_modify 1 format float %20.15g scale yes
dump_modify myDump image yes scale no flush yes
dump_modify 1 region mySphere thresh x &lt; 0.0 thresh epair &gt;= 3.2
dump_modify xtcdump precision 10000 sfactor 0.1
dump_modify 1 every 1000 nfile 20
dump_modify 1 every v_myVar
dump_modify 1 amap min max cf 0.0 3 min green 0.5 yellow max blue boxcolor red
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dump_modify</span> <span class="mi">1</span> <span class="nb">format</span> <span class="n">line</span> <span class="s2">&quot;</span><span class="si">%d</span><span class="s2"> </span><span class="si">%d</span><span class="s2"> </span><span class="si">%20.15g</span><span class="s2"> </span><span class="si">%g</span><span class="s2"> </span><span class="si">%g</span><span class="s2">&quot;</span> <span class="n">scale</span> <span class="n">yes</span>
<span class="n">dump_modify</span> <span class="mi">1</span> <span class="nb">format</span> <span class="nb">float</span> <span class="o">%</span><span class="mf">20.15</span><span class="n">g</span> <span class="n">scale</span> <span class="n">yes</span>
<span class="n">dump_modify</span> <span class="n">myDump</span> <span class="n">image</span> <span class="n">yes</span> <span class="n">scale</span> <span class="n">no</span> <span class="n">flush</span> <span class="n">yes</span>
<span class="n">dump_modify</span> <span class="mi">1</span> <span class="n">region</span> <span class="n">mySphere</span> <span class="n">thresh</span> <span class="n">x</span> <span class="o">&lt;</span> <span class="mf">0.0</span> <span class="n">thresh</span> <span class="n">epair</span> <span class="o">&gt;=</span> <span class="mf">3.2</span>
<span class="n">dump_modify</span> <span class="n">xtcdump</span> <span class="n">precision</span> <span class="mi">10000</span> <span class="n">sfactor</span> <span class="mf">0.1</span>
<span class="n">dump_modify</span> <span class="mi">1</span> <span class="n">every</span> <span class="mi">1000</span> <span class="n">nfile</span> <span class="mi">20</span>
<span class="n">dump_modify</span> <span class="mi">1</span> <span class="n">every</span> <span class="n">v_myVar</span>
<span class="n">dump_modify</span> <span class="mi">1</span> <span class="n">amap</span> <span class="nb">min</span> <span class="nb">max</span> <span class="n">cf</span> <span class="mf">0.0</span> <span class="mi">3</span> <span class="nb">min</span> <span class="n">green</span> <span class="mf">0.5</span> <span class="n">yellow</span> <span class="nb">max</span> <span class="n">blue</span> <span class="n">boxcolor</span> <span class="n">red</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -318,19 +318,19 @@ to the dump file. The <em>every</em> keyword cannot be used with the dump
<em>dcd</em> style.</p>
<p>For example, the following commands will
write snapshots at timesteps 0,10,20,30,100,200,300,1000,2000,etc:</p>
<pre class="literal-block">
variable s equal logfreq(10,3,10)
dump 1 all atom 100 tmp.dump
dump_modify 1 every v_s first yes
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">s</span> <span class="n">equal</span> <span class="n">logfreq</span><span class="p">(</span><span class="mi">10</span><span class="p">,</span><span class="mi">3</span><span class="p">,</span><span class="mi">10</span><span class="p">)</span>
<span class="n">dump</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">atom</span> <span class="mi">100</span> <span class="n">tmp</span><span class="o">.</span><span class="n">dump</span>
<span class="n">dump_modify</span> <span class="mi">1</span> <span class="n">every</span> <span class="n">v_s</span> <span class="n">first</span> <span class="n">yes</span>
</pre></div>
</div>
<p>The following commands would write snapshots at the timesteps listed
in file tmp.times:</p>
<pre class="literal-block">
variable f file tmp.times
variable s equal next(f)
dump 1 all atom 100 tmp.dump
dump_modify 1 every v_s
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">f</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">times</span>
<span class="n">variable</span> <span class="n">s</span> <span class="n">equal</span> <span class="nb">next</span><span class="p">(</span><span class="n">f</span><span class="p">)</span>
<span class="n">dump</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">atom</span> <span class="mi">100</span> <span class="n">tmp</span><span class="o">.</span><span class="n">dump</span>
<span class="n">dump_modify</span> <span class="mi">1</span> <span class="n">every</span> <span class="n">v_s</span>
</pre></div>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">When using a file-style variable with the <em>every</em> keyword, the
@ -406,11 +406,11 @@ an integer and you wish it to appear in the text dump file as a
(large) integer, then you need to use an appropriate format. For
example, these commands:</p>
</div>
<pre class="literal-block">
compute 1 all property/local batom1 batom2
dump 1 all local 100 tmp.bonds index c_1[1] c_1[2]
dump_modify 1 format &quot;%d %0.0f %0.0f&quot;
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">local</span> <span class="n">batom1</span> <span class="n">batom2</span>
<span class="n">dump</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">local</span> <span class="mi">100</span> <span class="n">tmp</span><span class="o">.</span><span class="n">bonds</span> <span class="n">index</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_1</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
<span class="n">dump_modify</span> <span class="mi">1</span> <span class="nb">format</span> <span class="s2">&quot;</span><span class="si">%d</span><span class="s2"> </span><span class="si">%0.0f</span><span class="s2"> </span><span class="si">%0.0f</span><span class="s2">&quot;</span>
</pre></div>
</div>
<p>will output the two atom IDs for atoms in each bond as integers. If
the dump_modify command were omitted, they would appear as
floating-point values, assuming they were large integers (more than 6
@ -566,7 +566,7 @@ atoms of each type will be drawn in the image.</p>
<p>The specified <em>type</em> should be an integer from 1 to Ntypes = the
number of atom types. A wildcard asterisk can be used in place of or
in conjunction with the <em>type</em> argument to specify a range of atom
types. This takes the form &#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or &#8220;m*n&#8221;. If N = the
types. This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or &#8220;m*n&#8221;. If N = the
number of atom types, then an asterisk with no numeric values means
all types from 1 to N. A leading asterisk means all types from 1 to n
(inclusive). A trailing asterisk means all types from n to N
@ -689,15 +689,15 @@ color map without having to specify where all the bin boundaries are.</p>
atoms in individual molecules with a different color. See the
examples/pour/in.pour.2d.molecule input script for an example of how
this is used.</p>
<pre class="literal-block">
variable colors string &amp;
<div class="highlight-default"><div class="highlight"><pre><span></span>variable colors string &amp;
&quot;red green blue yellow white &amp;
purple pink orange lime gray&quot;
variable mol atom mol%10
dump 1 all image 250 image.*.jpg v_mol type &amp;
zoom 1.6 adiam 1.5
dump_modify 1 pad 5 amap 0 10 sa 1 10 ${colors}
</pre>
dump_modify 1 pad 5 amap 0 10 sa 1 10 ${colors}
</pre></div>
</div>
<p>In this case, 10 colors are defined, and molecule IDs are
mapped to one of the colors, even if there are 1000s of molecules.</p>
<hr class="docutils" />
@ -711,7 +711,7 @@ set the color that bonds of each type will be drawn in the image.</p>
<p>The specified <em>type</em> should be an integer from 1 to Nbondtypes = the
number of bond types. A wildcard asterisk can be used in place of or
in conjunction with the <em>type</em> argument to specify a range of bond
types. This takes the form &#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or &#8220;m*n&#8221;. If N = the
types. This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or &#8220;m*n&#8221;. If N = the
number of bond types, then an asterisk with no numeric values means
all types from 1 to N. A leading asterisk means all types from 1 to n
(inclusive). A trailing asterisk means all types from n to N

14
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@ -156,11 +156,11 @@
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
fix 2 all atom/swap 1 1 29494 300.0 ke no types 1 2
fix myFix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6
fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 mu 0.0 4.3 -5.0
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">atom</span><span class="o">/</span><span class="n">swap</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">29494</span> <span class="mf">300.0</span> <span class="n">ke</span> <span class="n">no</span> <span class="n">types</span> <span class="mi">1</span> <span class="mi">2</span>
<span class="n">fix</span> <span class="n">myFix</span> <span class="nb">all</span> <span class="n">atom</span><span class="o">/</span><span class="n">swap</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">12345</span> <span class="mf">298.0</span> <span class="n">region</span> <span class="n">my_swap_region</span> <span class="n">types</span> <span class="mi">5</span> <span class="mi">6</span>
<span class="n">fix</span> <span class="n">SGMC</span> <span class="nb">all</span> <span class="n">atom</span><span class="o">/</span><span class="n">swap</span> <span class="mi">1</span> <span class="mi">100</span> <span class="mi">345</span> <span class="mf">1.0</span> <span class="n">semi</span><span class="o">-</span><span class="n">grand</span> <span class="n">yes</span> <span class="n">types</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">3</span> <span class="n">mu</span> <span class="mf">0.0</span> <span class="mf">4.3</span> <span class="o">-</span><span class="mf">5.0</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -250,7 +250,9 @@ system (the quantity used when performing GCMC moves),
you MUST enable the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option for
that fix. The doc pages for individual <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> commands
specify if this should be done.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>This fix writes the state of the fix to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. This includes information about the random
number generator seed, the next timestep for MC exchanges, etc. See
the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command for info on how to

52
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@ -140,22 +140,22 @@
one or more input values can be listed</li>
<li>value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[i], f_ID, f_ID[i], v_name</li>
</ul>
<pre class="literal-block">
x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
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, I can include wildcard (see below)
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, I can include wildcard (see below)
v_name = per-atom vector calculated by an atom-style variable with name
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">,</span><span class="n">z</span><span class="p">,</span><span class="n">vx</span><span class="p">,</span><span class="n">vy</span><span class="p">,</span><span class="n">vz</span><span class="p">,</span><span class="n">fx</span><span class="p">,</span><span class="n">fy</span><span class="p">,</span><span class="n">fz</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">attribute</span> <span class="p">(</span><span class="n">position</span><span class="p">,</span> <span class="n">velocity</span><span class="p">,</span> <span class="n">force</span> <span class="n">component</span><span class="p">)</span>
<span class="n">c_ID</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
<span class="n">c_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
<span class="n">f_ID</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
<span class="n">f_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
<span class="n">v_name</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">an</span> <span class="n">atom</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
fix 1 all ave/atom 1 100 100 vx vy vz
fix 1 all ave/atom 10 20 1000 c_my_stress[1]
fix 1 all ave/atom 10 20 1000 c_my_stress[*]
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">atom</span> <span class="mi">1</span> <span class="mi">100</span> <span class="mi">100</span> <span class="n">vx</span> <span class="n">vy</span> <span class="n">vz</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">atom</span> <span class="mi">10</span> <span class="mi">20</span> <span class="mi">1000</span> <span class="n">c_my_stress</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">atom</span> <span class="mi">10</span> <span class="mi">20</span> <span class="mi">1000</span> <span class="n">c_my_stress</span><span class="p">[</span><span class="o">*</span><span class="p">]</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -181,7 +181,7 @@ are the only ones that can be used with this fix since they produce
per-atom vectors.</p>
<p>Note that for values from a compute or fix, the bracketed index I can
be specified using a wildcard asterisk with the index to effectively
specify multiple values. This takes the form &#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or
specify multiple values. This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or
&#8220;m*n&#8221;. If N = the size of the vector (for <em>mode</em> = scalar) or the
number of columns in the array (for <em>mode</em> = vector), then an asterisk
with no numeric values means all indices from 1 to N. A leading
@ -192,13 +192,13 @@ means all indices from m to n (inclusive).</p>
had been listed one by one. E.g. these 2 fix ave/atom commands are
equivalent, since the <a class="reference internal" href="compute_stress_atom.html"><span class="doc">compute stress/atom</span></a>
command creates a per-atom array with 6 columns:</p>
<pre class="literal-block">
compute my_stress all stress/atom NULL
fix 1 all ave/atom 10 20 1000 c_my_stress[*]
fix 1 all ave/atom 10 20 1000 c_my_stress[1] c_my_stress[1] &amp;
c_my_stress[3] c_my_stress[4] &amp;
c_my_stress[5] c_my_stress[6]
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">my_stress</span> <span class="nb">all</span> <span class="n">stress</span><span class="o">/</span><span class="n">atom</span> <span class="n">NULL</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">atom</span> <span class="mi">10</span> <span class="mi">20</span> <span class="mi">1000</span> <span class="n">c_my_stress</span><span class="p">[</span><span class="o">*</span><span class="p">]</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">atom</span> <span class="mi">10</span> <span class="mi">20</span> <span class="mi">1000</span> <span class="n">c_my_stress</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_my_stress</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">&amp;</span>
<span class="n">c_my_stress</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">c_my_stress</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> <span class="o">&amp;</span>
<span class="n">c_my_stress</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span> <span class="n">c_my_stress</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span>
</pre></div>
</div>
<hr class="docutils" />
<p>The <em>Nevery</em>, <em>Nrepeat</em>, and <em>Nfreq</em> arguments specify on what
timesteps the input values will be used in order to contribute to the
@ -228,7 +228,7 @@ this is not what you want, consider averaging unwrapped coordinates,
which can be provided by the <a class="reference internal" href="compute_property_atom.html"><span class="doc">compute property/atom</span></a> command via its xu,yu,zu
attributes.</p>
</div>
<p>If a value begins with &#8220;c_&#8221;, a compute ID must follow which has been
<p>If a value begins with &#8220;<a href="#id1"><span class="problematic" id="id2">c_</span></a>&#8221;, a compute ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the per-atom vector calculated by the compute is used. If a
bracketed term containing an index I is appended, the Ith column of
@ -236,7 +236,7 @@ the per-atom array calculated by the compute is used. Users can also
write code for their own compute styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>. See the discussion above for how I can
be specified with a wildcard asterisk to effectively specify multiple
values.</p>
<p>If a value begins with &#8220;f_&#8221;, a fix ID must follow which has been
<p>If a value begins with &#8220;<a href="#id3"><span class="problematic" id="id4">f_</span></a>&#8221;, a fix ID must follow which has been
previously defined in the input script. If no bracketed term is
appended, the per-atom vector calculated by the fix is used. If a
bracketed term containing an index I is appended, the Ith column of
@ -246,13 +246,15 @@ compatible with <em>Nevery</em>, else an error will result. Users can also
write code for their own fix styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>. See the discussion above for how I can
be specified with a wildcard asterisk to effectively specify multiple
values.</p>
<p>If a value begins with &#8220;v_&#8221;, a variable name must follow which has
<p>If a value begins with &#8220;<a href="#id5"><span class="problematic" id="id6">v_</span></a>&#8221;, a variable name must follow which has
been previously defined in the input script as an <a class="reference internal" href="variable.html"><span class="doc">atom-style variable</span></a> Variables of style <em>atom</em> can reference
thermodynamic keywords, or invoke other computes, fixes, or variables
when they are evaluated, so this is a very general means of generating
per-atom quantities to time average.</p>
</div>
<hr class="docutils" />
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global scalar or vector quantities are
stored by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.</p>

54
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View File

@ -141,16 +141,16 @@
<li>one or more input values can be listed</li>
<li>value = vx, vy, vz, fx, fy, fz, density/mass, density/number, temp, c_ID, c_ID[I], f_ID, f_ID[I], v_name</li>
</ul>
<pre class="literal-block">
vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
density/number, density/mass = number or mass density
temp = temperature
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, I can include wildcard (see below)
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, I can include wildcard (see below)
v_name = per-atom vector calculated by an atom-style variable with name
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">vx</span><span class="p">,</span><span class="n">vy</span><span class="p">,</span><span class="n">vz</span><span class="p">,</span><span class="n">fx</span><span class="p">,</span><span class="n">fy</span><span class="p">,</span><span class="n">fz</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">attribute</span> <span class="p">(</span><span class="n">velocity</span><span class="p">,</span> <span class="n">force</span> <span class="n">component</span><span class="p">)</span>
<span class="n">density</span><span class="o">/</span><span class="n">number</span><span class="p">,</span> <span class="n">density</span><span class="o">/</span><span class="n">mass</span> <span class="o">=</span> <span class="n">number</span> <span class="ow">or</span> <span class="n">mass</span> <span class="n">density</span>
<span class="n">temp</span> <span class="o">=</span> <span class="n">temperature</span>
<span class="n">c_ID</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
<span class="n">c_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
<span class="n">f_ID</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
<span class="n">f_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
<span class="n">v_name</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">an</span> <span class="n">atom</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
</pre></div>
</div>
<ul class="simple">
<li>zero or more keyword/arg pairs may be appended</li>
<li>keyword = <em>norm</em> or <em>ave</em> or <em>bias</em> or <em>adof</em> or <em>cdof</em> or <em>file</em> or <em>overwrite</em> or <em>title1</em> or <em>title2</em> or <em>title3</em></li>
@ -185,12 +185,12 @@ v_name = per-atom vector calculated by an atom-style variable with name
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
fix 1 all ave/chunk 10000 1 10000 binchunk c_myCentro title1 &quot;My output values&quot;
fix 1 flow ave/chunk 100 10 1000 molchunk vx vz norm sample file vel.profile
fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running
fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">10000</span> <span class="mi">1</span> <span class="mi">10000</span> <span class="n">binchunk</span> <span class="n">c_myCentro</span> <span class="n">title1</span> <span class="s2">&quot;My output values&quot;</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="n">flow</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">100</span> <span class="mi">10</span> <span class="mi">1000</span> <span class="n">molchunk</span> <span class="n">vx</span> <span class="n">vz</span> <span class="n">norm</span> <span class="n">sample</span> <span class="n">file</span> <span class="n">vel</span><span class="o">.</span><span class="n">profile</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="n">flow</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">100</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="n">binchunk</span> <span class="n">density</span><span class="o">/</span><span class="n">mass</span> <span class="n">ave</span> <span class="n">running</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="n">flow</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">100</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="n">binchunk</span> <span class="n">density</span><span class="o">/</span><span class="n">mass</span> <span class="n">ave</span> <span class="n">running</span>
</pre></div>
</div>
<p><strong>NOTE:</strong></p>
<p>If you are trying to replace a deprectated fix ave/spatial command
with the newer, more flexible fix ave/chunk and <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> commands, you simply need to split
@ -242,7 +242,7 @@ ones that can be used with this fix since all other styles of variable
produce global quantities.</p>
<p>Note that for values from a compute or fix, the bracketed index I can
be specified using a wildcard asterisk with the index to effectively
specify multiple values. This takes the form &#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or
specify multiple values. This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or
&#8220;m*n&#8221;. If N = the size of the vector (for <em>mode</em> = scalar) or the
number of columns in the array (for <em>mode</em> = vector), then an asterisk
with no numeric values means all indices from 1 to N. A leading
@ -253,11 +253,11 @@ means all indices from m to n (inclusive).</p>
had been listed one by one. E.g. these 2 fix ave/chunk commands are
equivalent, since the <a class="reference internal" href="compute_property_atom.html"><span class="doc">compute property/atom</span></a> command creates, in this
case, a per-atom array with 3 columns:</p>
<pre class="literal-block">
compute myAng all property/atom angmomx angmomy angmomz
fix 1 all ave/chunk 100 1 100 cc1 c_myAng[*] file tmp.angmom
fix 2 all ave/chunk 100 1 100 cc1 c_myAng[1] c_myAng[2] c_myAng[3] file tmp.angmom
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">myAng</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">atom</span> <span class="n">angmomx</span> <span class="n">angmomy</span> <span class="n">angmomz</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">cc1</span> <span class="n">c_myAng</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">angmom</span>
<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">cc1</span> <span class="n">c_myAng</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_myAng</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_myAng</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">angmom</span>
</pre></div>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">This fix works by creating an array of size <em>Nchunk</em> by Nvalues
@ -349,7 +349,7 @@ in the chunk on different timesteps were collected together as one set
of atoms to calculate their temperature. The compute allows the
center-of-mass velocity of each chunk to be subtracted before
calculating the temperature; this fix does not.</p>
<p>If a value begins with &#8220;c_&#8221;, a compute ID must follow which has been
<p>If a value begins with &#8220;<a href="#id1"><span class="problematic" id="id2">c_</span></a>&#8221;, a compute ID must follow which has been
previously defined in the input script. If no bracketed integer is
appended, the per-atom vector calculated by the compute is used. If a
bracketed integer is appended, the Ith column of the per-atom array
@ -357,7 +357,7 @@ calculated by the compute is used. Users can also write code for
their own compute styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.
See the discussion above for how I can be specified with a wildcard
asterisk to effectively specify multiple values.</p>
<p>If a value begins with &#8220;f_&#8221;, a fix ID must follow which has been
<p>If a value begins with &#8220;<a href="#id3"><span class="problematic" id="id4">f_</span></a>&#8221;, a fix ID must follow which has been
previously defined in the input script. If no bracketed integer is
appended, the per-atom vector calculated by the fix is used. If a
bracketed integer is appended, the Ith column of the per-atom array
@ -367,7 +367,7 @@ their values on certain timesteps, which must be compatible with
own fix styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>. See the
discussion above for how I can be specified with a wildcard asterisk
to effectively specify multiple values.</p>
<p>If a value begins with &#8220;v_&#8221;, a variable name must follow which has
<p>If a value begins with &#8220;<a href="#id5"><span class="problematic" id="id6">v_</span></a>&#8221;, a variable name must follow which has
been previously defined in the input script. Variables of style
<em>atom</em> can reference thermodynamic keywords and various per-atom
attributes, or invoke other computes, fixes, or variables when they
@ -502,8 +502,10 @@ value of the <em>units</em> keyword is <em>reduced</em>, the coordinate values w
be in unitless reduced units (0-1). This is not true for the Coord1 value
of style <em>bin/sphere</em> or <em>bin/cylinder</em> which both represent radial
dimensions. Those values are always in distance <a class="reference internal" href="units.html"><span class="doc">units</span></a>.</p>
</div>
<hr class="docutils" />
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix.</p>
<p>This fix computes a global array of values which can be accessed by

30
doc/html/fix_ave_correlate_long.html
View File

@ -139,13 +139,13 @@
<li>one or more input values can be listed</li>
<li>value = c_ID, c_ID[N], f_ID, f_ID[N], v_name</li>
</ul>
<pre class="literal-block">
c_ID = global scalar calculated by a compute with ID
c_ID[I] = Ith component of global vector calculated by a compute with ID
f_ID = global scalar calculated by a fix with ID
f_ID[I] = Ith component of global vector calculated by a fix with ID
v_name = global value calculated by an equal-style variable with name
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">c_ID</span> <span class="o">=</span> <span class="k">global</span> <span class="n">scalar</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
<span class="n">c_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">component</span> <span class="n">of</span> <span class="k">global</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
<span class="n">f_ID</span> <span class="o">=</span> <span class="k">global</span> <span class="n">scalar</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
<span class="n">f_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">component</span> <span class="n">of</span> <span class="k">global</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
<span class="n">v_name</span> <span class="o">=</span> <span class="k">global</span> <span class="n">value</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">an</span> <span class="n">equal</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
</pre></div>
</div>
<ul class="simple">
<li>zero or more keyword/arg pairs may be appended</li>
<li>keyword = <em>type</em> or <em>start</em> or <em>file</em> or <em>overwrite</em> or <em>title1</em> or <em>title2</em> or <em>ncorr</em> or <em>p</em> or <em>m</em></li>
@ -177,12 +177,12 @@ v_name = global value calculated by an equal-style variable with name
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
fix 1 all ave/correlate/long 5 1000 c_myTemp file temp.correlate
fix 1 all ave/correlate/long 1 10000 &amp;
c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &amp;
type upper title1 &quot;My correlation data&quot; nlen 15 ncount 3
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">correlate</span><span class="o">/</span><span class="n">long</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="n">c_myTemp</span> <span class="n">file</span> <span class="n">temp</span><span class="o">.</span><span class="n">correlate</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">correlate</span><span class="o">/</span><span class="n">long</span> <span class="mi">1</span> <span class="mi">10000</span> <span class="o">&amp;</span>
<span class="n">c_thermo_press</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_thermo_press</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_thermo_press</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">&amp;</span>
<span class="nb">type</span> <span class="n">upper</span> <span class="n">title1</span> <span class="s2">&quot;My correlation data&quot;</span> <span class="n">nlen</span> <span class="mi">15</span> <span class="n">ncount</span> <span class="mi">3</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -221,7 +221,9 @@ steps can be calculated.</p>
4*ncorr*nlen*8 bytes. With the default values of the parameters, this
corresponds to about 10 KB.</p>
<p>For the meaning of the additional optional keywords, see the <a class="reference internal" href="fix_ave_correlate.html"><span class="doc">fix ave/correlate</span></a> doc page.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>Since this fix in intended for the calculation of time correlation
functions over very long MD simulations, the information about this
fix is written automatically to binary restart files, so that the time

54
doc/html/fix_ave_histo.html
View File

@ -145,15 +145,15 @@
<li>one or more input values can be listed</li>
<li>value = x, y, z, vx, vy, vz, fx, fy, fz, c_ID, c_ID[N], f_ID, f_ID[N], v_name</li>
</ul>
<pre class="literal-block">
x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
c_ID = scalar or vector calculated by a compute with ID
c_ID[I] = Ith component of vector or Ith column of array calculated by a compute with ID, I can include wildcard (see below)
f_ID = scalar or vector calculated by a fix with ID
f_ID[I] = Ith component of vector or Ith column of array calculated by a fix with ID, I can include wildcard (see below)
v_name = value(s) calculated by an equal-style or vector-style or atom-style variable with name
v_name[I] = value calculated by a vector-style variable with name
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">,</span><span class="n">z</span><span class="p">,</span><span class="n">vx</span><span class="p">,</span><span class="n">vy</span><span class="p">,</span><span class="n">vz</span><span class="p">,</span><span class="n">fx</span><span class="p">,</span><span class="n">fy</span><span class="p">,</span><span class="n">fz</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">attribute</span> <span class="p">(</span><span class="n">position</span><span class="p">,</span> <span class="n">velocity</span><span class="p">,</span> <span class="n">force</span> <span class="n">component</span><span class="p">)</span>
<span class="n">c_ID</span> <span class="o">=</span> <span class="n">scalar</span> <span class="ow">or</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
<span class="n">c_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">component</span> <span class="n">of</span> <span class="n">vector</span> <span class="ow">or</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
<span class="n">f_ID</span> <span class="o">=</span> <span class="n">scalar</span> <span class="ow">or</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
<span class="n">f_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">component</span> <span class="n">of</span> <span class="n">vector</span> <span class="ow">or</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
<span class="n">v_name</span> <span class="o">=</span> <span class="n">value</span><span class="p">(</span><span class="n">s</span><span class="p">)</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">an</span> <span class="n">equal</span><span class="o">-</span><span class="n">style</span> <span class="ow">or</span> <span class="n">vector</span><span class="o">-</span><span class="n">style</span> <span class="ow">or</span> <span class="n">atom</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
<span class="n">v_name</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">value</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">vector</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
</pre></div>
</div>
<ul class="simple">
<li>zero or more keyword/arg pairs may be appended</li>
<li>keyword = <em>mode</em> or <em>file</em> or <em>ave</em> or <em>start</em> or <em>beyond</em> or <em>overwrite</em> or <em>title1</em> or <em>title2</em> or <em>title3</em></li>
@ -185,13 +185,13 @@ v_name[I] = value calculated by a vector-style variable with name
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
fix 1 all ave/histo 100 5 1000 0.5 1.5 50 c_myTemp file temp.histo ave running
fix 1 all ave/histo 100 5 1000 -5 5 100 c_thermo_press[2] c_thermo_press[3] title1 &quot;My output values&quot;
fix 1 all ave/histo 100 5 1000 -5 5 100 c_thermo_press[*]
fix 1 all ave/histo 1 100 1000 -2.0 2.0 18 vx vy vz mode vector ave running beyond extra
fix 1 all ave/histo/weight 1 1 1 10 100 2000 c_XRD[1] c_XRD[2]
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">histo</span> <span class="mi">100</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="mf">0.5</span> <span class="mf">1.5</span> <span class="mi">50</span> <span class="n">c_myTemp</span> <span class="n">file</span> <span class="n">temp</span><span class="o">.</span><span class="n">histo</span> <span class="n">ave</span> <span class="n">running</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">histo</span> <span class="mi">100</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="o">-</span><span class="mi">5</span> <span class="mi">5</span> <span class="mi">100</span> <span class="n">c_thermo_press</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_thermo_press</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">title1</span> <span class="s2">&quot;My output values&quot;</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">histo</span> <span class="mi">100</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="o">-</span><span class="mi">5</span> <span class="mi">5</span> <span class="mi">100</span> <span class="n">c_thermo_press</span><span class="p">[</span><span class="o">*</span><span class="p">]</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">histo</span> <span class="mi">1</span> <span class="mi">100</span> <span class="mi">1000</span> <span class="o">-</span><span class="mf">2.0</span> <span class="mf">2.0</span> <span class="mi">18</span> <span class="n">vx</span> <span class="n">vy</span> <span class="n">vz</span> <span class="n">mode</span> <span class="n">vector</span> <span class="n">ave</span> <span class="n">running</span> <span class="n">beyond</span> <span class="n">extra</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">histo</span><span class="o">/</span><span class="n">weight</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">10</span> <span class="mi">100</span> <span class="mi">2000</span> <span class="n">c_XRD</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_XRD</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -232,7 +232,7 @@ with a bracketed term appended, indicating the Ith column of the array
is used.</p>
<p>Note that for values from a compute or fix, the bracketed index I can
be specified using a wildcard asterisk with the index to effectively
specify multiple values. This takes the form &#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or
specify multiple values. This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or
&#8220;m*n&#8221;. If N = the size of the vector (for <em>mode</em> = scalar) or the
number of columns in the array (for <em>mode</em> = vector), then an asterisk
with no numeric values means all indices from 1 to N. A leading
@ -243,11 +243,11 @@ means all indices from m to n (inclusive).</p>
vector or columns of the array had been listed one by one. E.g. these
2 fix ave/histo commands are equivalent, since the <a class="reference internal" href="compute_com_chunk.html"><span class="doc">compute com/chunk</span></a> command creates a global array with
3 columns:</p>
<pre class="literal-block">
compute myCOM all com/chunk
fix 1 all ave/histo 100 1 100 c_myCOM[*] file tmp1.com mode vector
fix 2 all ave/histo 100 1 100 c_myCOM[1] c_myCOM[2] c_myCOM[3] file tmp2.com mode vector
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">myCOM</span> <span class="nb">all</span> <span class="n">com</span><span class="o">/</span><span class="n">chunk</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">histo</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myCOM</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp1</span><span class="o">.</span><span class="n">com</span> <span class="n">mode</span> <span class="n">vector</span>
<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">histo</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myCOM</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_myCOM</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_myCOM</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp2</span><span class="o">.</span><span class="n">com</span> <span class="n">mode</span> <span class="n">vector</span>
</pre></div>
</div>
<p>If the fix ave/histo/weight command is used, exactly two values must
be specified. If the values are vectors, they must be the same
length. The first value (a scalar or vector) is what is histogrammed
@ -278,7 +278,7 @@ simply generated on timesteps 100,200,etc.</p>
self-explanatory. Note that other atom attributes can be used as
inputs to this fix by using the <a class="reference internal" href="compute_property_atom.html"><span class="doc">compute property/atom</span></a> command and then specifying
an input value from that compute.</p>
<p>If a value begins with &#8220;c_&#8221;, a compute ID must follow which has been
<p>If a value begins with &#8220;<a href="#id1"><span class="problematic" id="id2">c_</span></a>&#8221;, a compute ID must follow which has been
previously defined in the input script. If <em>mode</em> = scalar, then if
no bracketed term is appended, the global scalar calculated by the
compute is used. If a bracketed term is appended, the Ith element of
@ -295,7 +295,7 @@ can thus be accessed by fix ave/histo. Or it can be a compute defined
not in your input script, but by <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a> or other fixes such as <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> or <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a>. See
the doc pages for these commands which give the IDs of these computes.
Users can also write code for their own compute styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.</p>
<p>If a value begins with &#8220;f_&#8221;, a fix ID must follow which has been
<p>If a value begins with &#8220;<a href="#id3"><span class="problematic" id="id4">f_</span></a>&#8221;, a fix ID must follow which has been
previously defined in the input script. If <em>mode</em> = scalar, then if
no bracketed term is appended, the global scalar calculated by the fix
is used. If a bracketed term is appended, the Ith element of the
@ -309,7 +309,7 @@ values.</p>
<p>Note that some fixes only produce their values on certain timesteps,
which must be compatible with <em>Nevery</em>, else an error will result.
Users can also write code for their own fix styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.</p>
<p>If a value begins with &#8220;v_&#8221;, a variable name must follow which has
<p>If a value begins with &#8220;<a href="#id5"><span class="problematic" id="id6">v_</span></a>&#8221;, a variable name must follow which has
been previously defined in the input script. If <em>mode</em> = scalar, then
only equal-style or vector-style variables can be used, which both
produce global values. In this mode, a vector-style variable requires
@ -399,8 +399,10 @@ values for each of these, so they do not need to be specified.</p>
describes the six values that are printed at the first of each section
of output. The third describes the 4 values printed for each bin in
the histogram.</p>
</div>
<hr class="docutils" />
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix.</p>
<p>This fix produces a global vector and global array which can be

52
doc/html/fix_ave_time.html
View File

@ -140,14 +140,14 @@
<li>one or more input values can be listed</li>
<li>value = c_ID, c_ID[N], f_ID, f_ID[N], v_name</li>
</ul>
<pre class="literal-block">
c_ID = global scalar or vector calculated by a compute with ID
c_ID[I] = Ith component of global vector or Ith column of global array calculated by a compute with ID, I can include wildcard (see below)
f_ID = global scalar or vector calculated by a fix with ID
f_ID[I] = Ith component of global vector or Ith column of global array calculated by a fix with ID, I can include wildcard (see below)
v_name = value(s) calculated by an equal-style or vector-style variable with name
v_name[I] = value calculated by a vector-style variable with name
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">c_ID</span> <span class="o">=</span> <span class="k">global</span> <span class="n">scalar</span> <span class="ow">or</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
<span class="n">c_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">component</span> <span class="n">of</span> <span class="k">global</span> <span class="n">vector</span> <span class="ow">or</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="k">global</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
<span class="n">f_ID</span> <span class="o">=</span> <span class="k">global</span> <span class="n">scalar</span> <span class="ow">or</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
<span class="n">f_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">component</span> <span class="n">of</span> <span class="k">global</span> <span class="n">vector</span> <span class="ow">or</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="k">global</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span><span class="p">,</span> <span class="n">I</span> <span class="n">can</span> <span class="n">include</span> <span class="n">wildcard</span> <span class="p">(</span><span class="n">see</span> <span class="n">below</span><span class="p">)</span>
<span class="n">v_name</span> <span class="o">=</span> <span class="n">value</span><span class="p">(</span><span class="n">s</span><span class="p">)</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">an</span> <span class="n">equal</span><span class="o">-</span><span class="n">style</span> <span class="ow">or</span> <span class="n">vector</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
<span class="n">v_name</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">value</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">vector</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
</pre></div>
</div>
<ul class="simple">
<li>zero or more keyword/arg pairs may be appended</li>
<li>keyword = <em>mode</em> or <em>file</em> or <em>ave</em> or <em>start</em> or <em>off</em> or <em>overwrite</em> or <em>title1</em> or <em>title2</em> or <em>title3</em></li>
@ -179,13 +179,13 @@ v_name[I] = value calculated by a vector-style variable with name
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
fix 1 all ave/time 100 5 1000 c_myTemp c_thermo_temp file temp.profile
fix 1 all ave/time 100 5 1000 c_thermo_press[2] ave window 20 &amp;
title1 &quot;My output values&quot;
fix 1 all ave/time 100 5 1000 c_thermo_press[*]
fix 1 all ave/time 1 100 1000 f_indent f_indent[1] file temp.indent off 1
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="n">c_myTemp</span> <span class="n">c_thermo_temp</span> <span class="n">file</span> <span class="n">temp</span><span class="o">.</span><span class="n">profile</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="n">c_thermo_press</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">ave</span> <span class="n">window</span> <span class="mi">20</span> <span class="o">&amp;</span>
<span class="n">title1</span> <span class="s2">&quot;My output values&quot;</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">5</span> <span class="mi">1000</span> <span class="n">c_thermo_press</span><span class="p">[</span><span class="o">*</span><span class="p">]</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">1</span> <span class="mi">100</span> <span class="mi">1000</span> <span class="n">f_indent</span> <span class="n">f_indent</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">file</span> <span class="n">temp</span><span class="o">.</span><span class="n">indent</span> <span class="n">off</span> <span class="mi">1</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -228,7 +228,7 @@ is used. All vectors must be the same length, which is the length of
the vector or number of rows in the array.</p>
<p>Note that for values from a compute or fix, the bracketed index I can
be specified using a wildcard asterisk with the index to effectively
specify multiple values. This takes the form &#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or
specify multiple values. This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or
&#8220;m*n&#8221;. If N = the size of the vector (for <em>mode</em> = scalar) or the
number of columns in the array (for <em>mode</em> = vector), then an asterisk
with no numeric values means all indices from 1 to N. A leading
@ -239,11 +239,11 @@ means all indices from m to n (inclusive).</p>
vector or columns of the array had been listed one by one. E.g. these
2 fix ave/time commands are equivalent, since the <a class="reference internal" href="compute_rdf.html"><span class="doc">compute rdf</span></a> command creates, in this case, a global array
with 3 columns, each of length 50:</p>
<pre class="literal-block">
compute myRDF all rdf 50 1 2
fix 1 all ave/time 100 1 100 c_myRDF[*] file tmp1.rdf mode vector
fix 2 all ave/time 100 1 100 c_myRDF[1] c_myRDF[2] c_myRDF[3] file tmp2.rdf mode vector
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">myRDF</span> <span class="nb">all</span> <span class="n">rdf</span> <span class="mi">50</span> <span class="mi">1</span> <span class="mi">2</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myRDF</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp1</span><span class="o">.</span><span class="n">rdf</span> <span class="n">mode</span> <span class="n">vector</span>
<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">100</span> <span class="n">c_myRDF</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_myRDF</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_myRDF</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="n">file</span> <span class="n">tmp2</span><span class="o">.</span><span class="n">rdf</span> <span class="n">mode</span> <span class="n">vector</span>
</pre></div>
</div>
<hr class="docutils" />
<p>The <em>Nevery</em>, <em>Nrepeat</em>, and <em>Nfreq</em> arguments specify on what
timesteps the input values will be used in order to contribute to the
@ -261,7 +261,7 @@ timestep 200, etc. If Nrepeat=1 and Nfreq = 100, then no time
averaging is done; values are simply generated on timesteps
100,200,etc.</p>
<hr class="docutils" />
<p>If a value begins with &#8220;c_&#8221;, a compute ID must follow which has been
<p>If a value begins with &#8220;<a href="#id1"><span class="problematic" id="id2">c_</span></a>&#8221;, a compute ID must follow which has been
previously defined in the input script. If <em>mode</em> = scalar, then if
no bracketed term is appended, the global scalar calculated by the
compute is used. If a bracketed term is appended, the Ith element of
@ -277,7 +277,7 @@ can thus be accessed by fix ave/time. Or it can be a compute defined
not in your input script, but by <a class="reference internal" href="thermo_style.html"><span class="doc">thermodynamic output</span></a> or other fixes such as <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> or <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a>. See
the doc pages for these commands which give the IDs of these computes.
Users can also write code for their own compute styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.</p>
<p>If a value begins with &#8220;f_&#8221;, a fix ID must follow which has been
<p>If a value begins with &#8220;<a href="#id3"><span class="problematic" id="id4">f_</span></a>&#8221;, a fix ID must follow which has been
previously defined in the input script. If <em>mode</em> = scalar, then if
no bracketed term is appended, the global scalar calculated by the fix
is used. If a bracketed term is appended, the Ith element of the
@ -290,7 +290,7 @@ specify multiple values.</p>
<p>Note that some fixes only produce their values on certain timesteps,
which must be compatible with <em>Nevery</em>, else an error will result.
Users can also write code for their own fix styles and <a class="reference internal" href="Section_modify.html"><span class="doc">add them to LAMMPS</span></a>.</p>
<p>If a value begins with &#8220;v_&#8221;, a variable name must follow which has
<p>If a value begins with &#8220;<a href="#id5"><span class="problematic" id="id6">v_</span></a>&#8221;, a variable name must follow which has
been previously defined in the input script. If <em>mode</em> = scalar, then
only equal-style or vector-style variables can be used, which both
produce global values. In this mode, a vector-style variable requires
@ -383,8 +383,10 @@ so the <em>title3</em> setting is ignored when <em>mode</em> = scalar.</p>
describes the two values that are printed at the first of each section
of output. In the third line the values are replaced with the
appropriate fields from the fix ave/time command.</p>
</div>
<hr class="docutils" />
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix.</p>
<p>This fix produces a global scalar or global vector or global array

4
doc/html/fix_bond_break.html
View File

@ -224,8 +224,10 @@ dramatically released when the bond is broken. More generally, you
may need to thermostat your system to compensate for energy changes
resulting from broken bonds (and angles, dihedrals, impropers).</p>
</div>
</div>
<hr class="docutils" />
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix.</p>
<p>This fix computes two statistics which it stores in a global vector of

6
doc/html/fix_bond_create.html
View File

@ -265,7 +265,7 @@ percolation simulation.</p>
1st, 2nd, and 3rd neighbors of each atom (within the bond topology of
the system) for use in weighting pairwise interactions for bonded
atoms. Note that adding a single bond always adds a new 1st neighbor
but may also induce *many* new 2nd and 3rd neighbors, depending on the
but may also induce <em>many</em> new 2nd and 3rd neighbors, depending on the
molecular topology of your system. The &#8220;extra special per atom&#8221;
parameter must typically be set to allow for the new maximum total
size (1st + 2nd + 3rd neighbors) of this per-atom list. There are 3
@ -320,8 +320,10 @@ dramatically when the bond is formed. More generally, you may need to
thermostat your system to compensate for energy changes resulting from
created bonds (and angles, dihedrals, impropers).</p>
</div>
</div>
<hr class="docutils" />
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix.</p>
<p>This fix computes two statistics which it stores in a global vector of

4
doc/html/fix_colvars.html
View File

@ -200,7 +200,9 @@ wrapped back into the simulation cell at each re-neighboring instead.</p>
fix that thermostats all atoms in the fix colvars group. This will be
used to provide the colvars module with the current thermostat target
temperature.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>This fix writes the current status of the colvars module into
<a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. This is in addition to the text
mode status file that is written by the colvars module itself and the

68
doc/html/fix_deform.html
View File

@ -272,9 +272,9 @@ e.g. picoseconds for &#8220;metal&#8221; units). Tensile strain is unitless and
is defined as delta/L0, where L0 is the original box length and delta
is the change relative to the original length. The box length L as a
function of time will change as</p>
<pre class="literal-block">
L(t) = L0 (1 + erate*dt)
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">L</span><span class="p">(</span><span class="n">t</span><span class="p">)</span> <span class="o">=</span> <span class="n">L0</span> <span class="p">(</span><span class="mi">1</span> <span class="o">+</span> <span class="n">erate</span><span class="o">*</span><span class="n">dt</span><span class="p">)</span>
</pre></div>
</div>
<p>where dt is the elapsed time (in time units). Thus if <em>erate</em> R is
specified as 0.1 and time units are picoseconds, this means the box
length will increase by 10% of its original length every picosecond.
@ -295,9 +295,9 @@ e.g. picoseconds for &#8220;metal&#8221; units). Tensile strain is unitless and
is defined as delta/L0, where L0 is the original box length and delta
is the change relative to the original length.</p>
<p>The box length L as a function of time will change as</p>
<pre class="literal-block">
L(t) = L0 exp(trate*dt)
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">L</span><span class="p">(</span><span class="n">t</span><span class="p">)</span> <span class="o">=</span> <span class="n">L0</span> <span class="n">exp</span><span class="p">(</span><span class="n">trate</span><span class="o">*</span><span class="n">dt</span><span class="p">)</span>
</pre></div>
</div>
<p>where dt is the elapsed time (in time units). Thus if <em>trate</em> R is
specified as ln(1.1) and time units are picoseconds, this means the
box length will increase by 10% of its current (not original) length
@ -341,9 +341,9 @@ dimensions, so that they respond to the tensile strain dynamically.</p>
<p>The <em>wiggle</em> style oscillates the specified box length dimension
sinusoidally with the specified amplitude and period. I.e. the box
length L as a function of time is given by</p>
<pre class="literal-block">
L(t) = L0 + A sin(2*pi t/Tp)
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">L</span><span class="p">(</span><span class="n">t</span><span class="p">)</span> <span class="o">=</span> <span class="n">L0</span> <span class="o">+</span> <span class="n">A</span> <span class="n">sin</span><span class="p">(</span><span class="mi">2</span><span class="o">*</span><span class="n">pi</span> <span class="n">t</span><span class="o">/</span><span class="n">Tp</span><span class="p">)</span>
</pre></div>
</div>
<p>where L0 is its initial length. If the amplitude A is a positive
number the box initially expands, then contracts, etc. If A is
negative then the box initially contracts, then expands, etc. The
@ -370,13 +370,13 @@ arbitrary variable.</p>
<p>Here is an example of using the <em>variable</em> style to perform the same
box deformation as the <em>wiggle</em> style formula listed above, where we
assume that the current timestep = 0.</p>
<pre class="literal-block">
variable A equal 5.0
variable Tp equal 10.0
variable displace equal &quot;v_A * sin(2*PI * step*dt/v_Tp)&quot;
variable rate equal &quot;2*PI*v_A/v_Tp * cos(2*PI * step*dt/v_Tp)&quot;
fix 2 all deform 1 x variable v_displace v_rate remap v
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">A</span> <span class="n">equal</span> <span class="mf">5.0</span>
<span class="n">variable</span> <span class="n">Tp</span> <span class="n">equal</span> <span class="mf">10.0</span>
<span class="n">variable</span> <span class="n">displace</span> <span class="n">equal</span> <span class="s2">&quot;v_A * sin(2*PI * step*dt/v_Tp)&quot;</span>
<span class="n">variable</span> <span class="n">rate</span> <span class="n">equal</span> <span class="s2">&quot;2*PI*v_A/v_Tp * cos(2*PI * step*dt/v_Tp)&quot;</span>
<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">deform</span> <span class="mi">1</span> <span class="n">x</span> <span class="n">variable</span> <span class="n">v_displace</span> <span class="n">v_rate</span> <span class="n">remap</span> <span class="n">v</span>
</pre></div>
</div>
<p>For the <em>scale</em>, <em>vel</em>, <em>erate</em>, <em>trate</em>, <em>volume</em>, <em>wiggle</em>, and
<em>variable</em> styles, the box length is expanded or compressed around its
mid point.</p>
@ -413,9 +413,9 @@ to the shear direction (e.g. y box length for xy deformation) and
offset is the displacement distance in the shear direction (e.g. x
direction for xy deformation) from the unstrained orientation.</p>
<p>The tilt factor T as a function of time will change as</p>
<pre class="literal-block">
T(t) = T0 + L0*erate*dt
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">T</span><span class="p">(</span><span class="n">t</span><span class="p">)</span> <span class="o">=</span> <span class="n">T0</span> <span class="o">+</span> <span class="n">L0</span><span class="o">*</span><span class="n">erate</span><span class="o">*</span><span class="n">dt</span>
</pre></div>
</div>
<p>where T0 is the initial tilt factor, L0 is the original length of the
box perpendicular to the shear direction (e.g. y box length for xy
deformation), and dt is the elapsed time (in time units). Thus if
@ -441,9 +441,9 @@ where length is the box length perpendicular to the shear direction
distance in the shear direction (e.g. x direction for xy deformation)
from the unstrained orientation.</p>
<p>The tilt factor T as a function of time will change as</p>
<pre class="literal-block">
T(t) = T0 exp(trate*dt)
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">T</span><span class="p">(</span><span class="n">t</span><span class="p">)</span> <span class="o">=</span> <span class="n">T0</span> <span class="n">exp</span><span class="p">(</span><span class="n">trate</span><span class="o">*</span><span class="n">dt</span><span class="p">)</span>
</pre></div>
</div>
<p>where T0 is the initial tilt factor and dt is the elapsed time (in
time units). Thus if <em>trate</em> R is specified as ln(1.1) and time units
are picoseconds, this means the shear strain or tilt factor will
@ -464,9 +464,9 @@ parameter), then this effect on the shear strain is ignored.</p>
<p>The <em>wiggle</em> style oscillates the specified tilt factor sinusoidally
with the specified amplitude and period. I.e. the tilt factor T as a
function of time is given by</p>
<pre class="literal-block">
T(t) = T0 + A sin(2*pi t/Tp)
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">T</span><span class="p">(</span><span class="n">t</span><span class="p">)</span> <span class="o">=</span> <span class="n">T0</span> <span class="o">+</span> <span class="n">A</span> <span class="n">sin</span><span class="p">(</span><span class="mi">2</span><span class="o">*</span><span class="n">pi</span> <span class="n">t</span><span class="o">/</span><span class="n">Tp</span><span class="p">)</span>
</pre></div>
</div>
<p>where T0 is its initial value. If the amplitude A is a positive
number the tilt factor initially becomes more positive, then more
negative, etc. If A is negative then the tilt factor initially
@ -492,13 +492,13 @@ arbitrary variable.</p>
<p>Here is an example of using the <em>variable</em> style to perform the same
box deformation as the <em>wiggle</em> style formula listed above, where we
assume that the current timestep = 0.</p>
<pre class="literal-block">
variable A equal 5.0
variable Tp equal 10.0
variable displace equal &quot;v_A * sin(2*PI * step*dt/v_Tp)&quot;
variable rate equal &quot;2*PI*v_A/v_Tp * cos(2*PI * step*dt/v_Tp)&quot;
fix 2 all deform 1 xy variable v_displace v_rate remap v
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">A</span> <span class="n">equal</span> <span class="mf">5.0</span>
<span class="n">variable</span> <span class="n">Tp</span> <span class="n">equal</span> <span class="mf">10.0</span>
<span class="n">variable</span> <span class="n">displace</span> <span class="n">equal</span> <span class="s2">&quot;v_A * sin(2*PI * step*dt/v_Tp)&quot;</span>
<span class="n">variable</span> <span class="n">rate</span> <span class="n">equal</span> <span class="s2">&quot;2*PI*v_A/v_Tp * cos(2*PI * step*dt/v_Tp)&quot;</span>
<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">deform</span> <span class="mi">1</span> <span class="n">xy</span> <span class="n">variable</span> <span class="n">v_displace</span> <span class="n">v_rate</span> <span class="n">remap</span> <span class="n">v</span>
</pre></div>
</div>
<hr class="docutils" />
<p>All of the tilt styles change the xy, xz, yz tilt factors during a
simulation. In LAMMPS, tilt factors (xy,xz,yz) for triclinic boxes
@ -633,7 +633,9 @@ by including their suffix, or you can use the <a class="reference internal" href
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>.</p>

4
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View File

@ -355,7 +355,9 @@ count is changing due to adding particles, you typically should use
the <a class="reference internal" href="compute_modify.html"><span class="doc">compute_modify dynamic yes</span></a> command for the
temperature compute you are using.</p>
</div>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>This fix writes the state of the deposition to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. This includes information about how many
particles have been depositied, the random number generator seed, the
next timestep for deposition, etc. See the

4
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View File

@ -156,7 +156,9 @@ include that dimension in the distance calculation or force
application.</p>
<p>This command can be used to steer one or more atoms to a new location
in the simulation.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>respa</em> option is supported by this
fix. This allows to set at which level of the <a class="reference internal" href="run_style.html"><span class="doc">r-RESPA</span></a>

36
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View File

@ -219,14 +219,14 @@ Nose-Hoover thermostating fixes. The <em>fix drude/transform/inverse</em>
command must appear after any Nose-Hoover thermostating fixes.</p>
</div>
<p>Example:</p>
<pre class="literal-block">
fix fDIRECT all drude/transform/direct
fix fNVT gCORES nvt temp 300.0 300.0 100
fix fNVT gDRUDES nvt temp 1.0 1.0 100
fix fINVERSE all drude/transform/inverse
compute TDRUDE all temp/drude
thermo_style custom step cpu etotal ke pe ebond ecoul elong press vol temp c_TDRUDE[1] c_TDRUDE[2]
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">fDIRECT</span> <span class="nb">all</span> <span class="n">drude</span><span class="o">/</span><span class="n">transform</span><span class="o">/</span><span class="n">direct</span>
<span class="n">fix</span> <span class="n">fNVT</span> <span class="n">gCORES</span> <span class="n">nvt</span> <span class="n">temp</span> <span class="mf">300.0</span> <span class="mf">300.0</span> <span class="mi">100</span>
<span class="n">fix</span> <span class="n">fNVT</span> <span class="n">gDRUDES</span> <span class="n">nvt</span> <span class="n">temp</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mi">100</span>
<span class="n">fix</span> <span class="n">fINVERSE</span> <span class="nb">all</span> <span class="n">drude</span><span class="o">/</span><span class="n">transform</span><span class="o">/</span><span class="n">inverse</span>
<span class="n">compute</span> <span class="n">TDRUDE</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">drude</span>
<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">cpu</span> <span class="n">etotal</span> <span class="n">ke</span> <span class="n">pe</span> <span class="n">ebond</span> <span class="n">ecoul</span> <span class="n">elong</span> <span class="n">press</span> <span class="n">vol</span> <span class="n">temp</span> <span class="n">c_TDRUDE</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_TDRUDE</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
</pre></div>
</div>
<p>In this example, <em>gCORES</em> is the group of the atom cores and <em>gDRUDES</em>
is the group of the Drude particles (electrons). The centers of mass
of the Drude oscillators will be thermostated at 300.0 and the
@ -240,14 +240,14 @@ the other one should be <em>nvt</em>. You must add a <em>compute temp/com</em> a
that of its group (the Drude cores) but the pressure be the overall
pressure <em>thermo_press</em>.</p>
<p>Example:</p>
<pre class="literal-block">
compute cTEMP_CORE gCORES temp/com
fix fDIRECT all drude/transform/direct
fix fNPT gCORES npt temp 298.0 298.0 100 iso 1.0 1.0 500
fix_modify fNPT temp cTEMP_CORE press thermo_press
fix fNVT gDRUDES nvt temp 5.0 5.0 100
fix fINVERSE all drude/transform/inverse
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cTEMP_CORE</span> <span class="n">gCORES</span> <span class="n">temp</span><span class="o">/</span><span class="n">com</span>
<span class="n">fix</span> <span class="n">fDIRECT</span> <span class="nb">all</span> <span class="n">drude</span><span class="o">/</span><span class="n">transform</span><span class="o">/</span><span class="n">direct</span>
<span class="n">fix</span> <span class="n">fNPT</span> <span class="n">gCORES</span> <span class="n">npt</span> <span class="n">temp</span> <span class="mf">298.0</span> <span class="mf">298.0</span> <span class="mi">100</span> <span class="n">iso</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mi">500</span>
<span class="n">fix_modify</span> <span class="n">fNPT</span> <span class="n">temp</span> <span class="n">cTEMP_CORE</span> <span class="n">press</span> <span class="n">thermo_press</span>
<span class="n">fix</span> <span class="n">fNVT</span> <span class="n">gDRUDES</span> <span class="n">nvt</span> <span class="n">temp</span> <span class="mf">5.0</span> <span class="mf">5.0</span> <span class="mi">100</span>
<span class="n">fix</span> <span class="n">fINVERSE</span> <span class="nb">all</span> <span class="n">drude</span><span class="o">/</span><span class="n">transform</span><span class="o">/</span><span class="n">inverse</span>
</pre></div>
</div>
<p>In this example, <em>gCORES</em> is the group of the atom cores and <em>gDRUDES</em>
is the group of the Drude particles. The centers of mass of the Drude
oscillators will be thermostated at 298.0 and the internal degrees of
@ -259,8 +259,10 @@ to add a <em>fix momentum</em> command:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">fMOMENTUM</span> <span class="nb">all</span> <span class="n">momentum</span> <span class="mi">100</span> <span class="n">linear</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span>
</pre></div>
</div>
</div>
<hr class="docutils" />
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
</div>
<div class="section" id="restrictions">

12
doc/html/fix_efield.html
View File

@ -148,10 +148,10 @@
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
fix kick external-field efield 1.0 0.0 0.0
fix kick external-field efield 0.0 0.0 v_oscillate
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">kick</span> <span class="n">external</span><span class="o">-</span><span class="n">field</span> <span class="n">efield</span> <span class="mf">1.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span>
<span class="n">fix</span> <span class="n">kick</span> <span class="n">external</span><span class="o">-</span><span class="n">field</span> <span class="n">efield</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="n">v_oscillate</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -218,8 +218,10 @@ variable formulas, i.e. that -Grad(E) = F. For example, if the force
due to the electric field were a spring-like F = kx, then the energy
formula should be E = -0.5kx^2. If you don&#8217;t do this correctly, the
minimization will not converge properly.</p>
</div>
<hr class="docutils" />
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
fix to add the potential &#8220;energy&#8221; inferred by the added force due to

22
doc/html/fix_external.html
View File

@ -167,9 +167,9 @@ in the group, once every <em>Napply</em> steps, similar to the way the <a class=
<em>Napply</em>, the force values produced by one callback will persist, and
be used multiple times to update atom forces.</p>
<p>The callback function &#8220;foo&#8221; is invoked by the fix as:</p>
<pre class="literal-block">
foo(void *ptr, bigint timestep, int nlocal, int *ids, double **x, double **fexternal);
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">foo</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="n">ptr</span><span class="p">,</span> <span class="n">bigint</span> <span class="n">timestep</span><span class="p">,</span> <span class="nb">int</span> <span class="n">nlocal</span><span class="p">,</span> <span class="nb">int</span> <span class="o">*</span><span class="n">ids</span><span class="p">,</span> <span class="n">double</span> <span class="o">**</span><span class="n">x</span><span class="p">,</span> <span class="n">double</span> <span class="o">**</span><span class="n">fexternal</span><span class="p">);</span>
</pre></div>
</div>
<p>The arguments are as follows:</p>
<ul class="simple">
<li>ptr = pointer provided by and simply passed back to external driver</li>
@ -194,9 +194,9 @@ array. The fix adds these forces to each atom in the group, once
every <em>Napply</em> steps, similar to the way the <a class="reference internal" href="fix_addforce.html"><span class="doc">fix addforce</span></a> command works.</p>
<p>The name of the public force array provided by the FixExternal
class is</p>
<pre class="literal-block">
double **fexternal;
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">double</span> <span class="o">**</span><span class="n">fexternal</span><span class="p">;</span>
</pre></div>
</div>
<p>It is allocated by the FixExternal class as an (N,3) array where N is
the number of atoms owned by a processor. The 3 corresponds to the
fx, fy, fz components of force.</p>
@ -212,16 +212,18 @@ to the added forces must also be set so as to be consistent with the
added forces. Otherwise the minimization will not converge correctly.</p>
<p>This can be done from the external driver by calling this public
method of the FixExternal class:</p>
<pre class="literal-block">
void set_energy(double eng);
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">void</span> <span class="n">set_energy</span><span class="p">(</span><span class="n">double</span> <span class="n">eng</span><span class="p">);</span>
</pre></div>
</div>
<p>where eng is the potential energy. Eng is an extensive quantity,
meaning it should be the sum over per-atom energies of all affected
atoms. It should also be provided in <a class="reference internal" href="units.html"><span class="doc">energy units</span></a>
consistent with the simulation. See the details below for how to
insure this energy setting is used appropriately in a minimization.</p>
</div>
<hr class="docutils" />
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
fix to add the potential &#8220;energy&#8221; set by the external driver to the

32
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View File

@ -168,11 +168,11 @@ keyword = <em>mol</em>, <em>region</em>, <em>maxangle</em>, <em>pressure</em>, <
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
fix 2 gas gcmc 10 1000 1000 2 29494 298.0 -0.5 0.01
fix 3 water gcmc 10 100 100 0 3456543 3.0 -2.5 0.1 mol my_one_water maxangle 180 full_energy
fix 4 my_gas gcmc 1 10 10 1 123456543 300.0 -12.5 1.0 region disk
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">2</span> <span class="n">gas</span> <span class="n">gcmc</span> <span class="mi">10</span> <span class="mi">1000</span> <span class="mi">1000</span> <span class="mi">2</span> <span class="mi">29494</span> <span class="mf">298.0</span> <span class="o">-</span><span class="mf">0.5</span> <span class="mf">0.01</span>
<span class="n">fix</span> <span class="mi">3</span> <span class="n">water</span> <span class="n">gcmc</span> <span class="mi">10</span> <span class="mi">100</span> <span class="mi">100</span> <span class="mi">0</span> <span class="mi">3456543</span> <span class="mf">3.0</span> <span class="o">-</span><span class="mf">2.5</span> <span class="mf">0.1</span> <span class="n">mol</span> <span class="n">my_one_water</span> <span class="n">maxangle</span> <span class="mi">180</span> <span class="n">full_energy</span>
<span class="n">fix</span> <span class="mi">4</span> <span class="n">my_gas</span> <span class="n">gcmc</span> <span class="mi">1</span> <span class="mi">10</span> <span class="mi">10</span> <span class="mi">1</span> <span class="mi">123456543</span> <span class="mf">300.0</span> <span class="o">-</span><span class="mf">12.5</span> <span class="mf">1.0</span> <span class="n">region</span> <span class="n">disk</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -239,12 +239,12 @@ used in fix nvt. Otherwise, the imaginary reservoir
will not be in thermal equilibrium with the simulation cell. Also,
it is important that the temperature used by fix nvt be dynamic,
which can be achieved as follows:</p>
<pre class="literal-block">
compute mdtemp mdatoms temp
compute_modify mdtemp dynamic yes
fix mdnvt mdatoms nvt temp 300.0 300.0 10.0
fix_modify mdnvt temp mdtemp
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">mdtemp</span> <span class="n">mdatoms</span> <span class="n">temp</span>
<span class="n">compute_modify</span> <span class="n">mdtemp</span> <span class="n">dynamic</span> <span class="n">yes</span>
<span class="n">fix</span> <span class="n">mdnvt</span> <span class="n">mdatoms</span> <span class="n">nvt</span> <span class="n">temp</span> <span class="mf">300.0</span> <span class="mf">300.0</span> <span class="mf">10.0</span>
<span class="n">fix_modify</span> <span class="n">mdnvt</span> <span class="n">temp</span> <span class="n">mdtemp</span>
</pre></div>
</div>
<p>Note that neighbor lists are re-built every timestep that this fix is
invoked, so you should not set N to be too small. However, periodic
rebuilds are necessary in order to avoid dangerous rebuilds and missed
@ -363,9 +363,9 @@ therefore, you will want to use the
<a class="reference internal" href="compute_modify.html"><span class="doc">compute_modify</span></a> command to insure that the
current number of atoms is used as a normalizing factor each time
temperature is computed. Here is the necessary command:</p>
<pre class="literal-block">
compute_modify thermo_temp dynamic yes
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute_modify</span> <span class="n">thermo_temp</span> <span class="n">dynamic</span> <span class="n">yes</span>
</pre></div>
</div>
<p>If LJ units are used, note that a value of 0.18292026 is used by this
fix as the reduced value for Planck&#8217;s constant. This value was
derived from LJ parameters for argon, where h* = h/sqrt(sigma^2 *
@ -375,7 +375,9 @@ mass = 39.948 amu.</p>
of the group-ID value. The <em>grouptype</em> keyword assigns all
inserted atoms of the specified type to the <a class="reference internal" href="group.html"><span class="doc">group</span></a>
of the group-ID value.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>This fix writes the state of the fix to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. This includes information about the random
number generator seed, the next timestep for MC exchanges, etc. See
the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command for info on how to

6
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View File

@ -145,7 +145,7 @@
<dd><p class="first"><em>noneq</em> Cmatrix = file to read the non-equilibrium covariance matrix from
<em>every</em> stride = apply the GLE once every time steps. Reduces the accuracy</p>
<blockquote class="last">
<div>of the integration of the GLE, but has *no effect* on the accuracy of equilibrium
<div>of the integration of the GLE, but has <em>no effect</em> on the accuracy of equilibrium
sampling. It might change sampling properties when used together with <em>noneq</em>.</div></blockquote>
</dd>
</dl>
@ -207,7 +207,9 @@ Prony series form of the memory kernel used by GLD into an appropriate
input matrix for <a class="reference internal" href="#"><span class="doc">fix gle</span></a>. While the GLE scheme is more
general, the form used by <a class="reference internal" href="fix_gld.html"><span class="doc">fix gld</span></a> can be more directly
related to the representation of an implicit solvent environment.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>The instantaneous values of the extended variables are written to
<a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. Because the state of the random
number generator is not saved in restart files, this means you cannot

18
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View File

@ -156,13 +156,13 @@
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
fix 1 all gravity 1.0 chute 24.0
fix 1 all gravity v_increase chute 24.0
fix 1 all gravity 1.0 spherical 0.0 -180.0
fix 1 all gravity 10.0 spherical v_phi v_theta
fix 1 all gravity 100.0 vector 1 1 0
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">gravity</span> <span class="mf">1.0</span> <span class="n">chute</span> <span class="mf">24.0</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">gravity</span> <span class="n">v_increase</span> <span class="n">chute</span> <span class="mf">24.0</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">gravity</span> <span class="mf">1.0</span> <span class="n">spherical</span> <span class="mf">0.0</span> <span class="o">-</span><span class="mf">180.0</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">gravity</span> <span class="mf">10.0</span> <span class="n">spherical</span> <span class="n">v_phi</span> <span class="n">v_theta</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">gravity</span> <span class="mf">100.0</span> <span class="n">vector</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">0</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -220,8 +220,10 @@ by including their suffix, or you can use the <a class="reference internal" href
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
fix to add the gravitational potential energy of the system to the

14
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View File

@ -147,11 +147,11 @@
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
fix 3 qin heat 1 1.0
fix 3 qin heat 10 v_flux
fix 4 qout heat 1 -1.0 region top
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">3</span> <span class="n">qin</span> <span class="n">heat</span> <span class="mi">1</span> <span class="mf">1.0</span>
<span class="n">fix</span> <span class="mi">3</span> <span class="n">qin</span> <span class="n">heat</span> <span class="mi">10</span> <span class="n">v_flux</span>
<span class="n">fix</span> <span class="mi">4</span> <span class="n">qout</span> <span class="n">heat</span> <span class="mi">1</span> <span class="o">-</span><span class="mf">1.0</span> <span class="n">region</span> <span class="n">top</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -219,7 +219,9 @@ their velocities. Thus you must still use an integration fix
(e.g. <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a>) on the affected atoms. This fix should
not normally be used on atoms that have their temperature controlled
by another fix - e.g. <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt</span></a> or <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a> fix.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix.</p>
<p>This fix computes a global scalar which can be accessed by various

4
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@ -237,7 +237,9 @@ they were real objects. See the <a class="reference external" href="http://www.k
<p>If IMD control messages are received, a line of text describing the
message and its effect will be printed to the LAMMPS output screen, if
screen output is active.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global scalar or vector or per-atom
quantities are stored by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can

4
doc/html/fix_ipi.html
View File

@ -173,7 +173,9 @@ configurations make sense. It is assumed that the species in the i-PI
input are listed in the same order as in the data file of LAMMPS. The
initial configuration is ignored, as it will be substituted with the
coordinates received from i-PI before forces are ever evaluated.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>There is no restart information associated with this fix, since all
the dynamical parameters are dealt with by i-PI.</p>
</div>

4
doc/html/fix_langevin.html
View File

@ -375,8 +375,10 @@ by including their suffix, or you can use the <a class="reference internal" href
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. Because the state of the random number generator
is not saved in restart files, this means you cannot do &#8220;exact&#8221;
restarts with this fix, where the simulation continues on the same as

4
doc/html/fix_langevin_eff.html
View File

@ -178,7 +178,9 @@ interactions (<a class="reference internal" href="pair_style.html"><span class="
<p>The operation of this fix is exactly like that described by the <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a> command, except that the thermostatting
is also applied to the radial electron velocity for electron
particles.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. Because the state of the random number generator
is not saved in restart files, this means you cannot do &#8220;exact&#8221;
restarts with this fix, where the simulation continues on the same as

4
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View File

@ -167,7 +167,9 @@ and the fluid velocities at each lattice site.</p>
be changed by specifying the keyword <em>linear</em>, along with a set of
three flags set to 0/1 in order to exclude/ include the corresponding
dimension.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can be

4
doc/html/fix_lb_pc.html
View File

@ -149,7 +149,9 @@ described by <em>group-ID</em>, experiencing velocity-dependent hydrodynamic
forces, using the integration algorithm described in <a class="reference internal" href="fix_lb_viscous.html#mackay"><span class="std std-ref">Mackay et al.</span></a>. This integration algorithm should only be used if a
user-specified value for the force-coupling constant used in <a class="reference internal" href="fix_lb_fluid.html"><span class="doc">fix lb/fluid</span></a> has been set; do not use this integration
algorithm if the force coupling constant has been set by default.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can be

4
doc/html/fix_lb_rigid_pc_sphere.html
View File

@ -202,7 +202,9 @@ central atoms interact with one another.</p>
the rigid fix (although it includes fewer optional arguments, and
assumes the constituent atoms are point particles); see
<a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid</span></a> for a complete documentation.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>No information about the <em>rigid</em> and <em>rigid/nve</em> fixes are written to
<a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
<p>Similar to the <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid</span></a> command: The rigid

4
doc/html/fix_lb_viscous.html
View File

@ -164,8 +164,10 @@ hydrodynamic forces to the particles.</p>
test runs, see <a class="reference internal" href="#mackay"><span class="std std-ref">Mackay et al.</span></a>. Please include a citation to
this paper if this fix is used in work contributing to published
research.</p>
</div>
<hr class="docutils" />
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>As described in the <a class="reference internal" href="fix_viscous.html"><span class="doc">fix viscous</span></a> documentation:</p>
<p>&#8220;No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored

4
doc/html/fix_lineforce.html
View File

@ -151,7 +151,9 @@ remains. This is done by subtracting out components of force in the
plane perpendicular to the line.</p>
<p>If the initial velocity of the atom is 0.0 (or along the line), then
it should continue to move along the line thereafter.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can

38
doc/html/fix_move.html
View File

@ -160,11 +160,11 @@
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
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 class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="n">boundary</span> <span class="n">move</span> <span class="n">wiggle</span> <span class="mf">3.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">1.0</span> <span class="n">units</span> <span class="n">box</span>
<span class="n">fix</span> <span class="mi">2</span> <span class="n">boundary</span> <span class="n">move</span> <span class="n">rotate</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="mf">1.0</span> <span class="mf">5.0</span>
<span class="n">fix</span> <span class="mi">2</span> <span class="n">boundary</span> <span class="n">move</span> <span class="n">variable</span> <span class="n">v_myx</span> <span class="n">v_myy</span> <span class="n">NULL</span> <span class="n">v_VX</span> <span class="n">v_VY</span> <span class="n">NULL</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -202,9 +202,9 @@ command.</p>
<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>
<pre class="literal-block">
X(t) = X0 + V * delta
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><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
@ -216,17 +216,17 @@ 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"><span class="doc">equal-style variable</span></a> that uses the
vdisplace() function. E.g.</p>
<pre class="literal-block">
variable V equal 10.0
<div class="highlight-default"><div class="highlight"><pre><span></span>variable V equal 10.0
variable x equal vdisplace(0.0,$V)
fix 1 boundary move variable v_x NULL NULL v_V NULL NULL
</pre>
</pre></div>
</div>
<p>The <em>wiggle</em> style moves atoms in an oscillatory fashion, so that
their position <em>X</em> = (x,y,z) as a function of time is given in vector
notation as</p>
<pre class="literal-block">
X(t) = X0 + A sin(omega*delta)
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">X</span><span class="p">(</span><span class="n">t</span><span class="p">)</span> <span class="o">=</span> <span class="n">X0</span> <span class="o">+</span> <span class="n">A</span> <span class="n">sin</span><span class="p">(</span><span class="n">omega</span><span class="o">*</span><span class="n">delta</span><span class="p">)</span>
</pre></div>
</div>
<p>where <em>X0</em> = (x0,y0,z0) is their position at the time the fix is
specified, <em>A</em> is the specified amplitude vector with components
(Ax,Ay,Az), <em>omega</em> is 2 PI / <em>period</em>, and <em>delta</em> is the time
@ -239,14 +239,14 @@ corresponding force component on the atom.</p>
<p>Note that the <em>wiggle</em> style is identical to using the <em>variable</em>
style with <a class="reference internal" href="variable.html"><span class="doc">equal-style variables</span></a> that use the
swiggle() and cwiggle() functions. E.g.</p>
<pre class="literal-block">
variable A equal 10.0
<div class="highlight-default"><div class="highlight"><pre><span></span>variable A equal 10.0
variable T equal 5.0
variable omega equal 2.0*PI/$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>
</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. The direction of rotation for the
@ -302,8 +302,10 @@ are in lattice spacings. The <a class="reference internal" href="lattice.html">
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" />
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>This fix writes the original coordinates of moving atoms to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></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"><span class="doc">read_restart</span></a> command for info on how to re-specify

30
doc/html/fix_msst.html
View File

@ -197,14 +197,16 @@ LAMMPS, but are not implemented for MSST.</p>
<p>This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style &#8220;temp&#8221; and &#8220;pressure&#8221;,
as if these commands had been issued:</p>
<pre class="literal-block">
compute fix-ID_temp group-ID temp
compute fix-ID_press group-ID pressure fix-ID_temp
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">temp</span>
<span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_press</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">pressure</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span>
</pre></div>
</div>
<p>See the <a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a> and <a class="reference internal" href="compute_pressure.html"><span class="doc">compute pressure</span></a> commands for details. Note that the
IDs of the new computes are the fix-ID + underscore + &#8220;temp&#8221; or fix_ID
+ underscore + &#8220;press&#8221;. The group for the new computes is &#8220;all&#8221;.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>This fix writes the state of all internal variables to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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
@ -228,15 +230,15 @@ equations. See also <a class="reference internal" href="thermo_style.html"><span
</ol>
<p>To print these quantities to the log file with descriptive column
headers, the following LAMMPS commands are suggested:</p>
<pre class="literal-block">
fix msst all msst z
fix_modify msst energy yes
variable dhug equal f_msst[1]
variable dray equal f_msst[2]
variable lgr_vel equal f_msst[3]
variable lgr_pos equal f_msst[4]
thermo_style custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">msst</span> <span class="nb">all</span> <span class="n">msst</span> <span class="n">z</span>
<span class="n">fix_modify</span> <span class="n">msst</span> <span class="n">energy</span> <span class="n">yes</span>
<span class="n">variable</span> <span class="n">dhug</span> <span class="n">equal</span> <span class="n">f_msst</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span>
<span class="n">variable</span> <span class="n">dray</span> <span class="n">equal</span> <span class="n">f_msst</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span>
<span class="n">variable</span> <span class="n">lgr_vel</span> <span class="n">equal</span> <span class="n">f_msst</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span>
<span class="n">variable</span> <span class="n">lgr_pos</span> <span class="n">equal</span> <span class="n">f_msst</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span>
<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">ke</span> <span class="n">pe</span> <span class="n">lz</span> <span class="n">pzz</span> <span class="n">etotal</span> <span class="n">v_dhug</span> <span class="n">v_dray</span> <span class="n">v_lgr_vel</span> <span class="n">v_lgr_pos</span> <span class="n">f_msst</span>
</pre></div>
</div>
<p>These fixes compute a global scalar and a global vector of 4
quantities, which can be accessed by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. The scalar values calculated
by this fix are &#8220;extensive&#8221;; the vector values are &#8220;intensive&#8221;.</p>

4
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View File

@ -190,7 +190,9 @@ forces on atoms in this replica are described in the
</div>
<p>The inter-replica forces for the other replicas are unchanged from the
first equation.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can

10
doc/html/fix_nh_eff.html
View File

@ -134,9 +134,9 @@
<h1>fix nph/eff command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
fix ID group-ID style_name keyword value ...
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">style_name</span> <span class="n">keyword</span> <span class="n">value</span> <span class="o">...</span>
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
<li>style_name = <em>nvt/eff</em> or <em>npt/eff</em> or <em>nph/eff</em></li>
@ -223,7 +223,9 @@ degrees of freedom with the <a class="reference internal" href="velocity.html"><
the user must allow for these degrees of freedom to equilibrate
(i.e. equi-partitioning of energy) through time integration.</p>
</div>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>See the doc page for the <a class="reference internal" href="fix_nh.html"><span class="doc">fix nvt, npt, and nph</span></a> commands
for details.</p>
</div>

12
doc/html/fix_nph_asphere.html
View File

@ -175,10 +175,10 @@ unchanged and controlling the pressure of a surrounding fluid.</p>
<p>This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style &#8220;temp/asphere&#8221; and
&#8220;pressure&#8221;, as if these commands had been issued:</p>
<pre class="literal-block">
compute fix-ID_temp all temp/asphere
compute fix-ID_press all pressure fix-ID_temp
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">asphere</span>
<span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_press</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span>
</pre></div>
</div>
<p>See the <a class="reference internal" href="compute_temp_asphere.html"><span class="doc">compute temp/asphere</span></a> and <a class="reference internal" href="compute_pressure.html"><span class="doc">compute pressure</span></a> commands for details. Note that the
IDs of the new computes are the fix-ID + underscore + &#8220;temp&#8221; or fix_ID
+ underscore + &#8220;press&#8221;, and the group for the new computes is &#8220;all&#8221;
@ -207,7 +207,9 @@ by including their suffix, or you can use the <a class="reference internal" href
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>This fix writes the state of the Nose/Hoover barostat to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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

12
doc/html/fix_nph_sphere.html
View File

@ -175,10 +175,10 @@ unchanged and controlling the pressure of a surrounding fluid.</p>
<p>This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style &#8220;temp/sphere&#8221; and
&#8220;pressure&#8221;, as if these commands had been issued:</p>
<pre class="literal-block">
compute fix-ID_temp all temp/sphere
compute fix-ID_press all pressure fix-ID_temp
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">sphere</span>
<span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_press</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span>
</pre></div>
</div>
<p>See the <a class="reference internal" href="compute_temp_sphere.html"><span class="doc">compute temp/sphere</span></a> and <a class="reference internal" href="compute_pressure.html"><span class="doc">compute pressure</span></a> commands for details. Note that the
IDs of the new computes are the fix-ID + underscore + &#8220;temp&#8221; or fix_ID
+ underscore + &#8220;press&#8221;, and the group for the new computes is &#8220;all&#8221;
@ -207,7 +207,9 @@ by including their suffix, or you can use the <a class="reference internal" href
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>This fix writes the state of the Nose/Hoover barostat to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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

12
doc/html/fix_npt_asphere.html
View File

@ -182,10 +182,10 @@ unchanged and controlling the pressure of a surrounding fluid.</p>
<p>This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style &#8220;temp/asphere&#8221; and
&#8220;pressure&#8221;, as if these commands had been issued:</p>
<pre class="literal-block">
compute fix-ID_temp all temp/asphere
compute fix-ID_press all pressure fix-ID_temp
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">asphere</span>
<span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_press</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span>
</pre></div>
</div>
<p>See the <a class="reference internal" href="compute_temp_asphere.html"><span class="doc">compute temp/asphere</span></a> and <a class="reference internal" href="compute_pressure.html"><span class="doc">compute pressure</span></a> commands for details. Note that the
IDs of the new computes are the fix-ID + underscore + &#8220;temp&#8221; or fix_ID
+ underscore + &#8220;press&#8221;, and the group for the new computes is &#8220;all&#8221;
@ -227,7 +227,9 @@ by including their suffix, or you can use the <a class="reference internal" href
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>This fix writes the state of the Nose/Hoover thermostat and barostat
to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. See the
<a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command for info on how to re-specify

12
doc/html/fix_npt_body.html
View File

@ -179,10 +179,10 @@ unchanged and controlling the pressure of a surrounding fluid.</p>
<p>This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style &#8220;temp/body&#8221; and
&#8220;pressure&#8221;, as if these commands had been issued:</p>
<pre class="literal-block">
compute fix-ID_temp all temp/body
compute fix-ID_press all pressure fix-ID_temp
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">body</span>
<span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_press</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span>
</pre></div>
</div>
<p>See the <a class="reference internal" href="compute_temp_body.html"><span class="doc">compute temp/body</span></a> and <a class="reference internal" href="compute_pressure.html"><span class="doc">compute pressure</span></a> commands for details. Note that the
IDs of the new computes are the fix-ID + underscore + &#8220;temp&#8221; or fix_ID
+ underscore + &#8220;press&#8221;, and the group for the new computes is &#8220;all&#8221;
@ -224,7 +224,9 @@ by including their suffix, or you can use the <a class="reference internal" href
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>This fix writes the state of the Nose/Hoover thermostat and barostat
to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. See the
<a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command for info on how to re-specify

12
doc/html/fix_npt_sphere.html
View File

@ -181,10 +181,10 @@ unchanged and controlling the pressure of a surrounding fluid.</p>
<p>This fix computes a temperature and pressure each timestep. To do
this, the fix creates its own computes of style &#8220;temp/sphere&#8221; and
&#8220;pressure&#8221;, as if these commands had been issued:</p>
<pre class="literal-block">
compute fix-ID_temp all temp/sphere
compute fix-ID_press all pressure fix-ID_temp
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">sphere</span>
<span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_press</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span>
</pre></div>
</div>
<p>See the <a class="reference internal" href="compute_temp_sphere.html"><span class="doc">compute temp/sphere</span></a> and <a class="reference internal" href="compute_pressure.html"><span class="doc">compute pressure</span></a> commands for details. Note that the
IDs of the new computes are the fix-ID + underscore + &#8220;temp&#8221; or fix_ID
+ underscore + &#8220;press&#8221;, and the group for the new computes is &#8220;all&#8221;
@ -226,7 +226,9 @@ by including their suffix, or you can use the <a class="reference internal" href
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>This fix writes the state of the Nose/Hoover thermostat and barostat
to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. See the
<a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command for info on how to re-specify

4
doc/html/fix_nve_asphere.html
View File

@ -153,7 +153,9 @@ group each timestep. V is volume; E is energy. This creates a system
trajectory consistent with the microcanonical ensemble.</p>
<p>This fix differs from the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> command, which
assumes point particles and only updates their position and velocity.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can

4
doc/html/fix_nve_asphere_noforce.html
View File

@ -150,8 +150,10 @@ angularm momenta are used to update their positions and orientation.</p>
<p>This is useful as an implicit time integrator for Fast Lubrication
Dynamics, since the velocity and angular momentum are updated by the
<a class="reference external" href="pair_lubricateU.txt">pair_style lubricuteU</a> command.</p>
</div>
<hr class="docutils" />
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can

4
doc/html/fix_nve_body.html
View File

@ -151,7 +151,9 @@ consistent with the microcanonical ensemble. See <a class="reference internal"
doc page for more details on using body particles.</p>
<p>This fix differs from the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> command, which
assumes point particles and only updates their position and velocity.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can

4
doc/html/fix_nve_line.html
View File

@ -152,7 +152,9 @@ trajectory consistent with the microcanonical ensemble. See
using line segment particles.</p>
<p>This fix differs from the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> command, which
assumes point particles and only updates their position and velocity.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can

14
doc/html/fix_nve_manifold_rattle.html
View File

@ -159,7 +159,7 @@ keyword = <em>every</em>
atoms constrained to a curved surface (manifold) in the group each
timestep. The constraint is handled by RATTLE <a class="reference internal" href="fix_shake.html#andersen"><span class="std std-ref">(Andersen)</span></a>
written out for the special case of single-particle constraints as
explained in <a class="reference internal" href="#paquay"><span class="std std-ref">(Paquay)</span></a>. V is volume; E is energy. This way,
explained in <a class="reference internal" href="manifolds.html#paquay"><span class="std std-ref">(Paquay)</span></a>. V is volume; E is energy. This way,
the dynamics of particles constrained to curved surfaces can be
studied. If combined with <a class="reference internal" href="fix_langevin.html"><span class="doc">fix langevin</span></a>, this
generates Brownian motion of particles constrained to a curved
@ -172,18 +172,20 @@ manifolds this can be achieved with <em>region</em> and <em>create_atoms</em>
commands, but for more complex surfaces it might be more useful to
write a script.</p>
<p>The manifold args may be equal-style variables, like so:</p>
<pre class="literal-block">
variable R equal &quot;ramp(5.0,3.0)&quot;
fix shrink_sphere all nve/manifold/rattle 1e-4 10 sphere v_R
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">R</span> <span class="n">equal</span> <span class="s2">&quot;ramp(5.0,3.0)&quot;</span>
<span class="n">fix</span> <span class="n">shrink_sphere</span> <span class="nb">all</span> <span class="n">nve</span><span class="o">/</span><span class="n">manifold</span><span class="o">/</span><span class="n">rattle</span> <span class="mi">1</span><span class="n">e</span><span class="o">-</span><span class="mi">4</span> <span class="mi">10</span> <span class="n">sphere</span> <span class="n">v_R</span>
</pre></div>
</div>
<p>In this case, the manifold parameter will change in time according to
the variable. This is not a problem for the time integrator as long
as the change of the manifold is slow with respect to the dynamics of
the particles. Note that if the manifold has to exert work on the
particles because of these changes, the total energy might not be
conserved.</p>
</div>
<hr class="docutils" />
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can

4
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@ -189,8 +189,10 @@ by including their suffix, or you can use the <a class="reference internal" href
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can

4
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@ -152,7 +152,9 @@ trajectory consistent with the microcanonical ensemble. See
using triangular particles.</p>
<p>This fix differs from the <a class="reference internal" href="fix_nve.html"><span class="doc">fix nve</span></a> command, which
assumes point particles and only updates their position and velocity.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can

10
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@ -169,9 +169,9 @@ keywords.</p>
<p>This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style &#8220;temp/asphere&#8221;, as if this command
had been issued:</p>
<pre class="literal-block">
compute fix-ID_temp group-ID temp/asphere
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">temp</span><span class="o">/</span><span class="n">asphere</span>
</pre></div>
</div>
<p>See the <a class="reference internal" href="compute_temp_asphere.html"><span class="doc">compute temp/asphere</span></a> command for
details. Note that the ID of the new compute is the fix-ID +
underscore + &#8220;temp&#8221;, and the group for the new compute is the same as
@ -213,7 +213,9 @@ by including their suffix, or you can use the <a class="reference internal" href
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>This fix writes the state of the Nose/Hoover thermostat to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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

10
doc/html/fix_nvt_body.html
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@ -166,9 +166,9 @@ keywords.</p>
<p>This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style &#8220;temp/body&#8221;, as if this command
had been issued:</p>
<pre class="literal-block">
compute fix-ID_temp group-ID temp/body
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">temp</span><span class="o">/</span><span class="n">body</span>
</pre></div>
</div>
<p>See the <a class="reference internal" href="compute_temp_body.html"><span class="doc">compute temp/body</span></a> command for
details. Note that the ID of the new compute is the fix-ID +
underscore + &#8220;temp&#8221;, and the group for the new compute is the same as
@ -210,7 +210,9 @@ by including their suffix, or you can use the <a class="reference internal" href
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>This fix writes the state of the Nose/Hoover thermostat to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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

10
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@ -194,9 +194,9 @@ keywords.</p>
<p>This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style &#8220;temp/deform&#8221;, as if this command had
been issued:</p>
<pre class="literal-block">
compute fix-ID_temp group-ID temp/deform
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">temp</span><span class="o">/</span><span class="n">deform</span>
</pre></div>
</div>
<p>See the <a class="reference internal" href="compute_temp_deform.html"><span class="doc">compute temp/deform</span></a> command for
details. Note that the ID of the new compute is the fix-ID +
underscore + &#8220;temp&#8221;, and the group for the new compute is the same as
@ -238,7 +238,9 @@ by including their suffix, or you can use the <a class="reference internal" href
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>This fix writes the state of the Nose/Hoover thermostat to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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

4
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View File

@ -157,7 +157,9 @@ creates (as discussed in the <a class="reference internal" href="fix_nh.html"><s
page), is performed with a <a class="reference internal" href="compute_temp_deform_eff.html"><span class="doc">compute temp/deform/eff</span></a> commmand that includes
the eFF contribution to the temperature from the electron radial
velocity.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>This fix writes the state of the Nose/Hoover thermostat to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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

10
doc/html/fix_nvt_sphere.html
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@ -169,9 +169,9 @@ keywords.</p>
<p>This fix computes a temperature each timestep. To do this, the fix
creates its own compute of style &#8220;temp/sphere&#8221;, as if this command
had been issued:</p>
<pre class="literal-block">
compute fix-ID_temp group-ID temp/sphere
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">fix</span><span class="o">-</span><span class="n">ID_temp</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">temp</span><span class="o">/</span><span class="n">sphere</span>
</pre></div>
</div>
<p>See the <a class="reference internal" href="compute_temp_sphere.html"><span class="doc">compute temp/sphere</span></a> command for
details. Note that the ID of the new compute is the fix-ID +
underscore + &#8220;temp&#8221;, and the group for the new compute is the same as
@ -213,7 +213,9 @@ by including their suffix, or you can use the <a class="reference internal" href
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>This fix writes the state of the Nose/Hoover thermostat to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></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

10
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@ -128,9 +128,9 @@
<span id="index-0"></span><h1>fix phonon command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
fix ID group-ID phonon N Noutput Nwait map_file prefix keyword values ...
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">phonon</span> <span class="n">N</span> <span class="n">Noutput</span> <span class="n">Nwait</span> <span class="n">map_file</span> <span class="n">prefix</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span>
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
<li>phonon = style name of this fix command</li>
@ -239,7 +239,9 @@ even degrade the performance of lammps in case the unit cell is too large.</p>
<a class="reference internal" href="units.html"><span class="doc">energy/distance^2/mass</span></a> units. The coordinates for <em>q</em>
points in the log file is in the units of the basis vectors of the
corresponding reciprocal lattice.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>temp</em> option is supported by this
fix. You can use it to change the temperature compute from thermo_temp

4
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@ -316,8 +316,10 @@ can prevent particles from being inserted. The <em>ignore</em> keyword
causes the overlap check to skip any line or triangle particles.
Obviously you should only use it if there is in fact no overlap of the
line or triangle particles with the insertion region.</p>
</div>
<hr class="docutils" />
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. This means you must be careful when restarting a
pouring simulation, when the restart file was written in the middle of
the pouring operation. Specifically, you should use a new fix pour

18
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@ -162,13 +162,13 @@
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
fix 1 all qeq/point 1 10 1.0e-6 200 param.qeq1
fix 1 qeq qeq/shielded 1 8 1.0e-6 100 param.qeq2
fix 1 all qeq/slater 5 10 1.0e-6 100 params alpha 0.2
fix 1 qeq qeq/dynamic 1 12 1.0e-3 100 my_qeq
fix 1 all qeq/fire 1 10 1.0e-3 100 my_qeq qdamp 0.2 qstep 0.1
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">qeq</span><span class="o">/</span><span class="n">point</span> <span class="mi">1</span> <span class="mi">10</span> <span class="mf">1.0e-6</span> <span class="mi">200</span> <span class="n">param</span><span class="o">.</span><span class="n">qeq1</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="n">qeq</span> <span class="n">qeq</span><span class="o">/</span><span class="n">shielded</span> <span class="mi">1</span> <span class="mi">8</span> <span class="mf">1.0e-6</span> <span class="mi">100</span> <span class="n">param</span><span class="o">.</span><span class="n">qeq2</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">qeq</span><span class="o">/</span><span class="n">slater</span> <span class="mi">5</span> <span class="mi">10</span> <span class="mf">1.0e-6</span> <span class="mi">100</span> <span class="n">params</span> <span class="n">alpha</span> <span class="mf">0.2</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="n">qeq</span> <span class="n">qeq</span><span class="o">/</span><span class="n">dynamic</span> <span class="mi">1</span> <span class="mi">12</span> <span class="mf">1.0e-3</span> <span class="mi">100</span> <span class="n">my_qeq</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">qeq</span><span class="o">/</span><span class="n">fire</span> <span class="mi">1</span> <span class="mi">10</span> <span class="mf">1.0e-3</span> <span class="mi">100</span> <span class="n">my_qeq</span> <span class="n">qdamp</span> <span class="mf">0.2</span> <span class="n">qstep</span> <span class="mf">0.1</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -292,7 +292,9 @@ non-trivial. Charges on atoms are not guaranteed to equilibrate with
arbitrary choices of these parameters. We do not develop these QEq
paramters. See the examples/qeq directory for some examples.</p>
</div>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>No information about these fixes is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. No global scalar or vector or per-atom
quantities are stored by these fixes for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of these fixes
can be used with the <em>start/stop</em> keywords of the <a class="reference internal" href="run.html"><span class="doc">run</span></a>

4
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@ -195,8 +195,10 @@ by including their suffix, or you can use the <a class="reference internal" href
use the <a class="reference internal" href="suffix.html"><span class="doc">suffix</span></a> command in your input script.</p>
<p>See <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section_accelerate</span></a> of the manual for
more instructions on how to use the accelerated styles effectively.</p>
</div>
<hr class="docutils" />
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>respa</em> option is supported by this
fix. This allows to set at which level of the <a class="reference internal" href="run_style.html"><span class="doc">r-RESPA</span></a>

4
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@ -180,7 +180,9 @@ exponent. Note that these 3 quantities are also in the ReaxFF
potential file, except that eta is defined here as twice the eta value
in the ReaxFF file. Note that unlike the rest of LAMMPS, the units
of this fix are hard-coded to be A, eV, and electronic charge.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. No global scalar or vector or per-atom
quantities are stored by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can
be used with the <em>start/stop</em> keywords of the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command.</p>

4
doc/html/fix_qmmm.html
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@ -156,7 +156,9 @@ other QM codes. This will allow the LAMMPS side of the implementation
to be adapted if necessary before being finalized.</p>
<p>Details about how to use this fix are currently documented in the
description of the QM/MM interface code itself in lib/qmmm/README.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global scalar or vector or per-atom
quantities are stored by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can

14
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View File

@ -147,12 +147,12 @@
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
fix 1 all nve
fix 1 all qtb temp 110 damp 200 seed 35082 f_max 0.3 N_f 100 (liquid methane modeled with the REAX force field, real units)
fix 2 all nph iso 1.01325 1.01325 1
fix 2 all qtb temp 300 damp 1 seed 47508 f_max 120.0 N_f 100 (quartz modeled with the BKS force field, metal units)
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">nve</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">qtb</span> <span class="n">temp</span> <span class="mi">110</span> <span class="n">damp</span> <span class="mi">200</span> <span class="n">seed</span> <span class="mi">35082</span> <span class="n">f_max</span> <span class="mf">0.3</span> <span class="n">N_f</span> <span class="mi">100</span> <span class="p">(</span><span class="n">liquid</span> <span class="n">methane</span> <span class="n">modeled</span> <span class="k">with</span> <span class="n">the</span> <span class="n">REAX</span> <span class="n">force</span> <span class="n">field</span><span class="p">,</span> <span class="n">real</span> <span class="n">units</span><span class="p">)</span>
<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">nph</span> <span class="n">iso</span> <span class="mf">1.01325</span> <span class="mf">1.01325</span> <span class="mi">1</span>
<span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">qtb</span> <span class="n">temp</span> <span class="mi">300</span> <span class="n">damp</span> <span class="mi">1</span> <span class="n">seed</span> <span class="mi">47508</span> <span class="n">f_max</span> <span class="mf">120.0</span> <span class="n">N_f</span> <span class="mi">100</span> <span class="p">(</span><span class="n">quartz</span> <span class="n">modeled</span> <span class="k">with</span> <span class="n">the</span> <span class="n">BKS</span> <span class="n">force</span> <span class="n">field</span><span class="p">,</span> <span class="n">metal</span> <span class="n">units</span><span class="p">)</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -219,7 +219,7 @@ runs on different numbers of processors.</p>
vibrational modes with frequencies higher than <em>f_max</em> will not be
modulated. If we denote &amp;Delta;&lt;i&gt;t&lt;/i&gt; as the time interval for the
MD integration, <em>f_max</em> is always reset by the code to make
&lt;i&gt;&amp;alpha;&lt;/i&gt; = (int)(2*f_max*&amp;Delta;&lt;i&gt;t&lt;/i&gt;)&lt;sup&gt;&lt;i&gt;-1&lt;/i&gt;&lt;/sup&gt; a
&lt;i&gt;&amp;alpha;&lt;/i&gt; = (int)(2<em>f_max</em>&amp;Delta;&lt;i&gt;t&lt;/i&gt;)&lt;sup&gt;&lt;i&gt;-1&lt;/i&gt;&lt;/sup&gt; a
positive integer and print out relative information. An appropriate
value for the cutoff frequency <em>f_max</em> would be around 2~3
&lt;i&gt;f&lt;/i&gt;&lt;sub&gt;D&lt;/sub&gt;, where &lt;i&gt;f&lt;/i&gt;&lt;sub&gt;D&lt;/sub&gt; is the Debye

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@ -157,8 +157,10 @@ written to <em>filename</em> on timesteps that are multiples of <em>Nevery</em>,
including timestep 0. For time-averaged chemical species analysis,
please see the <a class="reference internal" href="fix_reaxc_species.html"><span class="doc">fix reaxc/c/species</span></a> command.</p>
<p>The format of the output file should be self-explantory.</p>
</div>
<hr class="docutils" />
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can

4
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@ -215,8 +215,10 @@ i.e. Nrepeat*Nevery can not exceed Nfreq.</p>
<p>For example, if Nevery=2, Nrepeat=6, and Nfreq=100, then bond-order
values on timesteps 90,92,94,96,98,100 will be used to compute the
average bond-order for the species analysis output on timestep 100.</p>
</div>
<hr class="docutils" />
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix.</p>
<p>This fix computes both a global vector of length 2 and a per-atom

60
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@ -128,9 +128,9 @@
<span id="index-0"></span><h1>fix saed/vtk command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
fix ID group-ID saed/vtk Nevery Nrepeat Nfreak c_ID attribute args ... keyword args ...
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">saed</span><span class="o">/</span><span class="n">vtk</span> <span class="n">Nevery</span> <span class="n">Nrepeat</span> <span class="n">Nfreak</span> <span class="n">c_ID</span> <span class="n">attribute</span> <span class="n">args</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">args</span> <span class="o">...</span>
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
<li>saed/vtk = style name of this fix command</li>
@ -154,14 +154,14 @@ keyword = <em>file</em> or <em>ave</em> or <em>start</em> or <em>file</em> or <e
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
compute 1 all saed 0.0251 Al O Kmax 1.70 Zone 0 0 1 dR_Ewald 0.01 c 0.5 0.5 0.5
compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo
</pre>
<pre class="literal-block">
fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed
fix saed/vtk 1 1 1 c_2 file Ni_000.saed
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">saed</span> <span class="mf">0.0251</span> <span class="n">Al</span> <span class="n">O</span> <span class="n">Kmax</span> <span class="mf">1.70</span> <span class="n">Zone</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">1</span> <span class="n">dR_Ewald</span> <span class="mf">0.01</span> <span class="n">c</span> <span class="mf">0.5</span> <span class="mf">0.5</span> <span class="mf">0.5</span>
<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">saed</span> <span class="mf">0.0251</span> <span class="n">Ni</span> <span class="n">Kmax</span> <span class="mf">1.70</span> <span class="n">Zone</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="n">c</span> <span class="mf">0.05</span> <span class="mf">0.05</span> <span class="mf">0.05</span> <span class="n">manual</span> <span class="n">echo</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">saed</span><span class="o">/</span><span class="n">vtk</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">c_1</span> <span class="n">file</span> <span class="n">Al2O3_001</span><span class="o">.</span><span class="n">saed</span>
<span class="n">fix</span> <span class="n">saed</span><span class="o">/</span><span class="n">vtk</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">c_2</span> <span class="n">file</span> <span class="n">Ni_000</span><span class="o">.</span><span class="n">saed</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -182,10 +182,10 @@ specified values may represent calculations performed by saed computes
which store their own &#8220;group&#8221; definitions.</p>
<p>Fix saed/vtk is designed to work only with <a class="reference internal" href="compute_saed.html"><span class="doc">compute saed</span></a>
values, e.g.</p>
<pre class="literal-block">
compute 3 top saed 0.0251 Al O
fix saed/vtk 1 1 1 c_3 file Al2O3_001.saed
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="mi">3</span> <span class="n">top</span> <span class="n">saed</span> <span class="mf">0.0251</span> <span class="n">Al</span> <span class="n">O</span>
<span class="n">fix</span> <span class="n">saed</span><span class="o">/</span><span class="n">vtk</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">c_3</span> <span class="n">file</span> <span class="n">Al2O3_001</span><span class="o">.</span><span class="n">saed</span>
</pre></div>
</div>
<hr class="docutils" />
<p>The <em>Nevery</em>, <em>Nrepeat</em>, and <em>Nfreq</em> arguments specify on what
timesteps the input values will be used in order to contribute to the
@ -209,19 +209,19 @@ vtk image data formatting. The filename assigned by the <em>file</em> keyword i
appended with _N.vtk where N is an index (0,1,2...) to account for multiple
diffraction intensity outputs.</p>
<p>By default the header contains the following information (with example data):</p>
<pre class="literal-block">
# vtk DataFile Version 3.0 c_SAED
Image data set
ASCII
DATASET STRUCTURED_POINTS
DIMENSIONS 337 219 209
ASPECT_RATIO 0.00507953 0.00785161 0.00821458
ORIGIN -0.853361 -0.855826 -0.854316
POINT_DATA 15424827
SCALARS intensity float
LOOKUP_TABLE default
...data
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># vtk DataFile Version 3.0 c_SAED</span>
<span class="n">Image</span> <span class="n">data</span> <span class="nb">set</span>
<span class="n">ASCII</span>
<span class="n">DATASET</span> <span class="n">STRUCTURED_POINTS</span>
<span class="n">DIMENSIONS</span> <span class="mi">337</span> <span class="mi">219</span> <span class="mi">209</span>
<span class="n">ASPECT_RATIO</span> <span class="mf">0.00507953</span> <span class="mf">0.00785161</span> <span class="mf">0.00821458</span>
<span class="n">ORIGIN</span> <span class="o">-</span><span class="mf">0.853361</span> <span class="o">-</span><span class="mf">0.855826</span> <span class="o">-</span><span class="mf">0.854316</span>
<span class="n">POINT_DATA</span> <span class="mi">15424827</span>
<span class="n">SCALARS</span> <span class="n">intensity</span> <span class="nb">float</span>
<span class="n">LOOKUP_TABLE</span> <span class="n">default</span>
<span class="o">...</span><span class="n">data</span>
</pre></div>
</div>
<p>In this example, kspace is sampled across a 337 x 219 x 209 point mesh
where the mesh spacing is approximately 0.005, 0.007, and 0.008
inv(length) units in the k1, k2, and k3 directions, respectively.
@ -264,7 +264,9 @@ intensity outputs.</p>
<p>The <em>overwrite</em> keyword will continuously overwrite the output file
with the latest output, so that it only contains one timestep worth of
output. This option can only be used with the <em>ave running</em> setting.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix.</p>
<p>No parameter of this fix can be used with the <em>start/stop</em> keywords of

4
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@ -212,7 +212,9 @@ over the pulling force in direction of the spring is recorded and
can then later be used to compute the potential of mean force (PMF)
by averaging over multiple independent trajectories along the same
pulling path.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>The fix stores the direction of the spring, current pulling target
distance and the running PMF to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.
See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command for info on how to

16
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@ -128,9 +128,9 @@
<span id="index-0"></span><h1>fix smd/adjust_dt command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
fix ID group-ID smd/adjust_dt arg
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">smd</span><span class="o">/</span><span class="n">adjust_dt</span> <span class="n">arg</span>
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
<li>smd/adjust_dt = style name of this fix command</li>
@ -142,9 +142,9 @@ fix ID group-ID smd/adjust_dt arg
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
fix 1 all smd/adjust_dt 0.1
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">smd</span><span class="o">/</span><span class="n">adjust_dt</span> <span class="mf">0.1</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -157,7 +157,9 @@ stable maximum time step.</p>
<p>This fix inquires the minimum stable time increment across all particles contained in the group for which this
fix is defined. An additional safety factor <em>s_fact</em> is applied to the time increment.</p>
<p>See <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</a> to use Smooth Mach Dynamics in LAMMPS.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>Currently, no part of USER-SMD supports restarting nor minimization.</p>
</div>
<div class="section" id="restrictions">

18
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@ -128,9 +128,9 @@
<span id="index-0"></span><h1>fix smd/integrate_tlsph command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
fix ID group-ID smd/integrate_tlsph keyword values
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">smd</span><span class="o">/</span><span class="n">integrate_tlsph</span> <span class="n">keyword</span> <span class="n">values</span>
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
<li>smd/integrate_tlsph = style name of this fix command</li>
@ -144,10 +144,10 @@ fix ID group-ID smd/integrate_tlsph keyword values
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
fix 1 all smd/integrate_tlsph
fix 1 all smd/integrate_tlsph limit_velocity 1000
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">smd</span><span class="o">/</span><span class="n">integrate_tlsph</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">smd</span><span class="o">/</span><span class="n">integrate_tlsph</span> <span class="n">limit_velocity</span> <span class="mi">1000</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -155,7 +155,9 @@ fix 1 all smd/integrate_tlsph limit_velocity 1000
<p>See <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</a> to using Smooth Mach Dynamics in LAMMPS.</p>
<p>The <em>limit_velocity</em> keyword will control the velocity, scaling the norm of
the velocity vector to max_vel in case it exceeds this velocity limit.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.</p>
</div>
<div class="section" id="restrictions">

24
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@ -128,9 +128,9 @@
<span id="index-0"></span><h1>fix smd/integrate_ulsph command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
fix ID group-ID smd/integrate_ulsph keyword
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">smd</span><span class="o">/</span><span class="n">integrate_ulsph</span> <span class="n">keyword</span>
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
<li>smd/integrate_ulsph = style name of this fix command</li>
@ -148,12 +148,12 @@ max_nn = maximum number of neighbors</dd>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
fix 1 all smd/integrate_ulsph adjust_radius 1.02 25 50
</pre>
<pre class="literal-block">
fix 1 all smd/integrate_ulsph limit_velocity 1000
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">smd</span><span class="o">/</span><span class="n">integrate_ulsph</span> <span class="n">adjust_radius</span> <span class="mf">1.02</span> <span class="mi">25</span> <span class="mi">50</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">smd</span><span class="o">/</span><span class="n">integrate_ulsph</span> <span class="n">limit_velocity</span> <span class="mi">1000</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -161,10 +161,12 @@ fix 1 all smd/integrate_ulsph limit_velocity 1000
See <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</a> to using Smooth Mach Dynamics in LAMMPS.</p>
<p>The <em>adjust_radius</em> keyword activates dynamic adjustment of the per-particle SPH smoothing kernel radius such that the number of neighbors per particles remains
within the interval <em>min_nn</em> to <em>max_nn</em>. The parameter <em>adjust_radius_factor</em> determines the amount of adjustment per timestep. Typical values are
<a href="#id1"><span class="problematic" id="id2">*</span></a>adjust_radius_factor*=1.02, <a href="#id3"><span class="problematic" id="id4">*</span></a>min_nn*=15, and <a href="#id5"><span class="problematic" id="id6">*</span></a>max_nn*=20.</p>
<em>adjust_radius_factor</em>=1.02, <em>min_nn</em>=15, and <em>max_nn</em>=20.</p>
<p>The <em>limit_velocity</em> keyword will control the velocity, scaling the norm of
the velocity vector to max_vel in case it exceeds this velocity limit.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.</p>
</div>
<div class="section" id="restrictions">

50
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@ -128,53 +128,55 @@
<span id="index-0"></span><h1>fix smd/move_tri_surf command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
fix ID group-ID smd/move_tri_surf keyword
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">smd</span><span class="o">/</span><span class="n">move_tri_surf</span> <span class="n">keyword</span>
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
<li>smd/move_tri_surf keyword = style name of this fix command</li>
<li>keyword = <em>*LINEAR</em> or <em>*WIGGLE</em> or <em>*ROTATE</em></li>
<li>keyword = <a href="#id1"><span class="problematic" id="id2">**</span></a>LINEAR* or <a href="#id3"><span class="problematic" id="id4">**</span></a>WIGGLE* or <a href="#id5"><span class="problematic" id="id6">**</span></a>ROTATE*</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 = Vx Vy Vz max_travel
vx,vy,vz = components of velocity vector (velocity units), any component can be specified as NULL
max_travel = wiggle amplitude
<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)
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">**</span><span class="n">LINEAR</span><span class="o">*</span> <span class="n">args</span> <span class="o">=</span> <span class="n">Vx</span> <span class="n">Vy</span> <span class="n">Vz</span>
<span class="n">Vx</span><span class="p">,</span><span class="n">Vy</span><span class="p">,</span><span class="n">Vz</span> <span class="o">=</span> <span class="n">components</span> <span class="n">of</span> <span class="n">velocity</span> <span class="n">vector</span> <span class="p">(</span><span class="n">velocity</span> <span class="n">units</span><span class="p">),</span> <span class="nb">any</span> <span class="n">component</span> <span class="n">can</span> <span class="n">be</span> <span class="n">specified</span> <span class="k">as</span> <span class="n">NULL</span>
<span class="o">**</span><span class="n">WIGGLE</span><span class="o">*</span> <span class="n">args</span> <span class="o">=</span> <span class="n">Vx</span> <span class="n">Vy</span> <span class="n">Vz</span> <span class="n">max_travel</span>
<span class="n">vx</span><span class="p">,</span><span class="n">vy</span><span class="p">,</span><span class="n">vz</span> <span class="o">=</span> <span class="n">components</span> <span class="n">of</span> <span class="n">velocity</span> <span class="n">vector</span> <span class="p">(</span><span class="n">velocity</span> <span class="n">units</span><span class="p">),</span> <span class="nb">any</span> <span class="n">component</span> <span class="n">can</span> <span class="n">be</span> <span class="n">specified</span> <span class="k">as</span> <span class="n">NULL</span>
<span class="n">max_travel</span> <span class="o">=</span> <span class="n">wiggle</span> <span class="n">amplitude</span>
<span class="o">**</span><span class="n">ROTATE</span><span class="o">*</span> <span class="n">args</span> <span class="o">=</span> <span class="n">Px</span> <span class="n">Py</span> <span class="n">Pz</span> <span class="n">Rx</span> <span class="n">Ry</span> <span class="n">Rz</span> <span class="n">period</span>
<span class="n">Px</span><span class="p">,</span><span class="n">Py</span><span class="p">,</span><span class="n">Pz</span> <span class="o">=</span> <span class="n">origin</span> <span class="n">point</span> <span class="n">of</span> <span class="n">axis</span> <span class="n">of</span> <span class="n">rotation</span> <span class="p">(</span><span class="n">distance</span> <span class="n">units</span><span class="p">)</span>
<span class="n">Rx</span><span class="p">,</span><span class="n">Ry</span><span class="p">,</span><span class="n">Rz</span> <span class="o">=</span> <span class="n">axis</span> <span class="n">of</span> <span class="n">rotation</span> <span class="n">vector</span>
<span class="n">period</span> <span class="o">=</span> <span class="n">period</span> <span class="n">of</span> <span class="n">rotation</span> <span class="p">(</span><span class="n">time</span> <span class="n">units</span><span class="p">)</span>
</pre></div>
</div>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
fix 1 tool smd/move_tri_surf *LINEAR 20 20 10
fix 2 tool smd/move_tri_surf *WIGGLE 20 20 10
fix 2 tool smd/move_tri_surf *ROTATE 0 0 0 5 2 1
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="n">tool</span> <span class="n">smd</span><span class="o">/</span><span class="n">move_tri_surf</span> <span class="o">*</span><span class="n">LINEAR</span> <span class="mi">20</span> <span class="mi">20</span> <span class="mi">10</span>
<span class="n">fix</span> <span class="mi">2</span> <span class="n">tool</span> <span class="n">smd</span><span class="o">/</span><span class="n">move_tri_surf</span> <span class="o">*</span><span class="n">WIGGLE</span> <span class="mi">20</span> <span class="mi">20</span> <span class="mi">10</span>
<span class="n">fix</span> <span class="mi">2</span> <span class="n">tool</span> <span class="n">smd</span><span class="o">/</span><span class="n">move_tri_surf</span> <span class="o">*</span><span class="n">ROTATE</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">5</span> <span class="mi">2</span> <span class="mi">1</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>This fix applies only to rigid surfaces read from .STL files via fix <a class="reference internal" href="fix_smd_wall_surface.html"><span class="doc">smd/wall_surface</span></a> .
It updates position and velocity for the particles in the group each timestep without regard to forces on the particles.
The rigid surfaces can thus be moved along simple trajectories during the simulation.</p>
<p>The <em>*LINEAR</em> style moves particles with the specified constant velocity
<p>The <a href="#id19"><span class="problematic" id="id20">**</span></a>LINEAR* style moves particles with the specified constant velocity
vector V = (Vx,Vy,Vz). This style also sets the velocity of each particle
to V = (Vx,Vy,Vz).</p>
<p>The <em>*WIGGLE</em> style moves particles in an oscillatory fashion.
<p>The <a href="#id21"><span class="problematic" id="id22">**</span></a>WIGGLE* style moves particles in an oscillatory fashion.
Particles are moved along (vx, vy, vz) with constant velocity until a
displacement of max_travel is reached. Then, the velocity vector is
reversed. This process is repeated.</p>
<p>The <em>*ROTATE</em> style rotates particles around a rotation axis R = (Rx,Ry,Rz) that
<p>The <a href="#id23"><span class="problematic" id="id24">**</span></a>ROTATE* style rotates particles around a rotation axis R = (Rx,Ry,Rz) that
goes through a point P = (Px,Py,Pz). The period of the rotation is also
specified. This style also sets the velocity of each particle 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 particle.</p>
<p>See <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</a> to using Smooth Mach Dynamics in LAMMPS.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.</p>
</div>
<div class="section" id="restrictions">

10
doc/html/fix_smd_setvel.html
View File

@ -146,9 +146,9 @@
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
fix top_velocity top_group setvel 1.0 0.0 0.0
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">top_velocity</span> <span class="n">top_group</span> <span class="n">setvel</span> <span class="mf">1.0</span> <span class="mf">0.0</span> <span class="mf">0.0</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -174,8 +174,10 @@ coordinates. Thus it is easy to specify a spatially-dependent velocity
field with optional time-dependence as well.</p>
<p>If the <em>region</em> keyword is used, the particle must also be in the
specified geometric <a class="reference internal" href="region.html"><span class="doc">region</span></a> in order to have its velocity set by this command.</p>
</div>
<hr class="docutils" />
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>Currently, no part of USER-SMD supports restarting nor minimization
None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix.</p>

16
doc/html/fix_smd_wall_surface.html
View File

@ -128,9 +128,9 @@
<span id="index-0"></span><h1>fix smd/wall_surface command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
fix ID group-ID smd/wall_surface arg type mol-ID
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">smd</span><span class="o">/</span><span class="n">wall_surface</span> <span class="n">arg</span> <span class="nb">type</span> <span class="n">mol</span><span class="o">-</span><span class="n">ID</span>
</pre></div>
</div>
<ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="fix.html"><span class="doc">fix</span></a> command</li>
<li>smd/wall_surface = style name of this fix command</li>
@ -146,9 +146,9 @@ fix ID group-ID smd/wall_surface arg type mol-ID
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<pre class="literal-block">
fix stl_surf all smd/wall_surface tool.stl 2 65535
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">stl_surf</span> <span class="nb">all</span> <span class="n">smd</span><span class="o">/</span><span class="n">wall_surface</span> <span class="n">tool</span><span class="o">.</span><span class="n">stl</span> <span class="mi">2</span> <span class="mi">65535</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -160,7 +160,9 @@ It is possible to move the triangulated surface via the <a class="reference inte
<p>Immediately after a .STL file has been read, the simulation needs to be run for 0 timesteps in order to properly register the new particles
in the system. See the &#8220;funnel_flow&#8221; example in the USER-SMD examples directory.</p>
<p>See <a class="reference external" href="USER/smd/SMD_LAMMPS_userguide.pdf">this PDF guide</a> to use Smooth Mach Dynamics in LAMMPS.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>Currently, no part of USER-SMD supports restarting nor minimization. This fix has no outputs.</p>
</div>
<div class="section" id="restrictions">

4
doc/html/fix_spring.html
View File

@ -215,7 +215,9 @@ spring command, if the rigid body will cross a periodic boundary.
This is because image flags for rigid bodies are used in a different
way, as explained on the <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid</span></a> doc page.</p>
</div>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
fix to add the energy stored in the spring to the system&#8217;s potential

4
doc/html/fix_spring_chunk.html
View File

@ -166,7 +166,9 @@ the mass of the atom, and Mm is the total mass of all atoms in the
chunk. Note that <em>K</em> thus represents the spring constant for the
total force on each chunk of atoms, not for a spring applied to each
atom.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>energy</em> option is supported by this
fix to add the energy stored in all the springs to the system&#8217;s potential

4
doc/html/fix_spring_self.html
View File

@ -160,7 +160,9 @@ spring force is applied. By default, the restraint is applied in all
directions, but it can be limited to the xy-, xz-, yz-plane and the
x-, y-, or z-direction, thus restraining the atoms to a line or a
plane, respectively.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>This fix writes the original coordinates of tethered atoms to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>, so that the spring effect will be the
same in a restarted simulation. See the
<a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command for info on how to re-specify

78
doc/html/fix_store_state.html
View File

@ -137,43 +137,43 @@
<li>N = store atom attributes every N steps, N = 0 for initial store only</li>
<li>input = one or more atom attributes</li>
</ul>
<pre class="literal-block">
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>
<pre class="literal-block">
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 class="highlight-default"><div class="highlight"><pre><span></span><span class="n">possible</span> <span class="n">attributes</span> <span class="o">=</span> <span class="nb">id</span><span class="p">,</span> <span class="n">mol</span><span class="p">,</span> <span class="nb">type</span><span class="p">,</span> <span class="n">mass</span><span class="p">,</span>
<span class="n">x</span><span class="p">,</span> <span class="n">y</span><span class="p">,</span> <span class="n">z</span><span class="p">,</span> <span class="n">xs</span><span class="p">,</span> <span class="n">ys</span><span class="p">,</span> <span class="n">zs</span><span class="p">,</span> <span class="n">xu</span><span class="p">,</span> <span class="n">yu</span><span class="p">,</span> <span class="n">zu</span><span class="p">,</span> <span class="n">xsu</span><span class="p">,</span> <span class="n">ysu</span><span class="p">,</span> <span class="n">zsu</span><span class="p">,</span> <span class="n">ix</span><span class="p">,</span> <span class="n">iy</span><span class="p">,</span> <span class="n">iz</span><span class="p">,</span>
<span class="n">vx</span><span class="p">,</span> <span class="n">vy</span><span class="p">,</span> <span class="n">vz</span><span class="p">,</span> <span class="n">fx</span><span class="p">,</span> <span class="n">fy</span><span class="p">,</span> <span class="n">fz</span><span class="p">,</span>
<span class="n">q</span><span class="p">,</span> <span class="n">mux</span><span class="p">,</span> <span class="n">muy</span><span class="p">,</span> <span class="n">muz</span><span class="p">,</span> <span class="n">mu</span><span class="p">,</span>
<span class="n">radius</span><span class="p">,</span> <span class="n">diameter</span><span class="p">,</span> <span class="n">omegax</span><span class="p">,</span> <span class="n">omegay</span><span class="p">,</span> <span class="n">omegaz</span><span class="p">,</span>
<span class="n">angmomx</span><span class="p">,</span> <span class="n">angmomy</span><span class="p">,</span> <span class="n">angmomz</span><span class="p">,</span> <span class="n">tqx</span><span class="p">,</span> <span class="n">tqy</span><span class="p">,</span> <span class="n">tqz</span><span class="p">,</span>
<span class="n">c_ID</span><span class="p">,</span> <span class="n">c_ID</span><span class="p">[</span><span class="n">N</span><span class="p">],</span> <span class="n">f_ID</span><span class="p">,</span> <span class="n">f_ID</span><span class="p">[</span><span class="n">N</span><span class="p">],</span> <span class="n">v_name</span><span class="p">,</span>
<span class="n">d_name</span><span class="p">,</span> <span class="n">i_name</span>
</pre></div>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="nb">id</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">ID</span>
<span class="n">mol</span> <span class="o">=</span> <span class="n">molecule</span> <span class="n">ID</span>
<span class="nb">type</span> <span class="o">=</span> <span class="n">atom</span> <span class="nb">type</span>
<span class="n">mass</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">mass</span>
<span class="n">x</span><span class="p">,</span><span class="n">y</span><span class="p">,</span><span class="n">z</span> <span class="o">=</span> <span class="n">unscaled</span> <span class="n">atom</span> <span class="n">coordinates</span>
<span class="n">xs</span><span class="p">,</span><span class="n">ys</span><span class="p">,</span><span class="n">zs</span> <span class="o">=</span> <span class="n">scaled</span> <span class="n">atom</span> <span class="n">coordinates</span>
<span class="n">xu</span><span class="p">,</span><span class="n">yu</span><span class="p">,</span><span class="n">zu</span> <span class="o">=</span> <span class="n">unwrapped</span> <span class="n">atom</span> <span class="n">coordinates</span>
<span class="n">xsu</span><span class="p">,</span><span class="n">ysu</span><span class="p">,</span><span class="n">zsu</span> <span class="o">=</span> <span class="n">scaled</span> <span class="n">unwrapped</span> <span class="n">atom</span> <span class="n">coordinates</span>
<span class="n">ix</span><span class="p">,</span><span class="n">iy</span><span class="p">,</span><span class="n">iz</span> <span class="o">=</span> <span class="n">box</span> <span class="n">image</span> <span class="n">that</span> <span class="n">the</span> <span class="n">atom</span> <span class="ow">is</span> <span class="ow">in</span>
<span class="n">vx</span><span class="p">,</span><span class="n">vy</span><span class="p">,</span><span class="n">vz</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">velocities</span>
<span class="n">fx</span><span class="p">,</span><span class="n">fy</span><span class="p">,</span><span class="n">fz</span> <span class="o">=</span> <span class="n">forces</span> <span class="n">on</span> <span class="n">atoms</span>
<span class="n">q</span> <span class="o">=</span> <span class="n">atom</span> <span class="n">charge</span>
<span class="n">mux</span><span class="p">,</span><span class="n">muy</span><span class="p">,</span><span class="n">muz</span> <span class="o">=</span> <span class="n">orientation</span> <span class="n">of</span> <span class="n">dipolar</span> <span class="n">atom</span>
<span class="n">mu</span> <span class="o">=</span> <span class="n">magnitued</span> <span class="n">of</span> <span class="n">dipole</span> <span class="n">moment</span> <span class="n">of</span> <span class="n">atom</span>
<span class="n">radius</span><span class="p">,</span><span class="n">diameter</span> <span class="o">=</span> <span class="n">radius</span><span class="o">.</span><span class="n">diameter</span> <span class="n">of</span> <span class="n">spherical</span> <span class="n">particle</span>
<span class="n">omegax</span><span class="p">,</span><span class="n">omegay</span><span class="p">,</span><span class="n">omegaz</span> <span class="o">=</span> <span class="n">angular</span> <span class="n">velocity</span> <span class="n">of</span> <span class="n">spherical</span> <span class="n">particle</span>
<span class="n">angmomx</span><span class="p">,</span><span class="n">angmomy</span><span class="p">,</span><span class="n">angmomz</span> <span class="o">=</span> <span class="n">angular</span> <span class="n">momentum</span> <span class="n">of</span> <span class="n">aspherical</span> <span class="n">particle</span>
<span class="n">tqx</span><span class="p">,</span><span class="n">tqy</span><span class="p">,</span><span class="n">tqz</span> <span class="o">=</span> <span class="n">torque</span> <span class="n">on</span> <span class="n">finite</span><span class="o">-</span><span class="n">size</span> <span class="n">particles</span>
<span class="n">c_ID</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
<span class="n">c_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">compute</span> <span class="k">with</span> <span class="n">ID</span>
<span class="n">f_ID</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
<span class="n">f_ID</span><span class="p">[</span><span class="n">I</span><span class="p">]</span> <span class="o">=</span> <span class="n">Ith</span> <span class="n">column</span> <span class="n">of</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">array</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">a</span> <span class="n">fix</span> <span class="k">with</span> <span class="n">ID</span>
<span class="n">v_name</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">vector</span> <span class="n">calculated</span> <span class="n">by</span> <span class="n">an</span> <span class="n">atom</span><span class="o">-</span><span class="n">style</span> <span class="n">variable</span> <span class="k">with</span> <span class="n">name</span>
<span class="n">d_name</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">floating</span> <span class="n">point</span> <span class="n">vector</span> <span class="n">name</span><span class="p">,</span> <span class="n">managed</span> <span class="n">by</span> <span class="n">fix</span> <span class="nb">property</span><span class="o">/</span><span class="n">atom</span>
<span class="n">i_name</span> <span class="o">=</span> <span class="n">per</span><span class="o">-</span><span class="n">atom</span> <span class="n">integer</span> <span class="n">vector</span> <span class="n">name</span><span class="p">,</span> <span class="n">managed</span> <span class="n">by</span> <span class="n">fix</span> <span class="nb">property</span><span class="o">/</span><span class="n">atom</span>
</pre></div>
</div>
<ul class="simple">
<li>zero or more keyword/value pairs may be appended</li>
<li>keyword = <em>com</em></li>
@ -217,7 +217,9 @@ 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>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>This fix writes the per-atom values it stores to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>, so that the values can be restored when a
simulation is restarted. See the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a>
command for info on how to re-specify a fix in an input script that

4
doc/html/fix_temp_rescale_eff.html
View File

@ -154,7 +154,9 @@ their velocities.</p>
<p>The operation of this fix is exactly like that described by the <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a> command, except that the rescaling
is also applied to the radial electron velocity for electron
particles.</p>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
<p>The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> <em>temp</em> option is supported by this
fix. You can use it to assign a temperature <a class="reference internal" href="compute.html"><span class="doc">compute</span></a>

4
doc/html/fix_tfmc.html
View File

@ -228,8 +228,10 @@ translations or rotations of the fix group could be induced by these
external forces, and removing them will lead to a violation of
detailed balance.</p>
</div>
</div>
<hr class="docutils" />
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>.</p>
<p>None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options are relevant to this
fix.</p>

16
doc/html/fix_thermal_conductivity.html
View File

@ -180,12 +180,12 @@ of the 2 atoms is performed, to conserve kinetic energy. Over time,
this induces a temperature gradient in the system which can be
measured using commands such as the following, which writes the
temperature profile (assuming z = edim) to the file tmp.profile:</p>
<pre class="literal-block">
compute ke all ke/atom
variable temp atom c_ke/1.5
compute layers all chunk/atom bin/1d z lower 0.05 units reduced
fix 3 all ave/chunk 10 100 1000 layers v_temp file tmp.profile
</pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ke</span> <span class="nb">all</span> <span class="n">ke</span><span class="o">/</span><span class="n">atom</span>
<span class="n">variable</span> <span class="n">temp</span> <span class="n">atom</span> <span class="n">c_ke</span><span class="o">/</span><span class="mf">1.5</span>
<span class="n">compute</span> <span class="n">layers</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="nb">bin</span><span class="o">/</span><span class="mi">1</span><span class="n">d</span> <span class="n">z</span> <span class="n">lower</span> <span class="mf">0.05</span> <span class="n">units</span> <span class="n">reduced</span>
<span class="n">fix</span> <span class="mi">3</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">chunk</span> <span class="mi">10</span> <span class="mi">100</span> <span class="mi">1000</span> <span class="n">layers</span> <span class="n">v_temp</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">profile</span>
</pre></div>
</div>
<p>Note that by default, Nswap = 1, though this can be changed by the
optional <em>swap</em> keyword. Setting this parameter appropriately, in
conjunction with the swap rate N, allows the heat flux to be adjusted
@ -221,7 +221,9 @@ not in a regime of linear response. In this case you cannot
accurately infer a thermal conductivity and should try increasing the
Nevery parameter.</p>
</div>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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</h2>
<p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix.</p>
<p>This fix computes a global scalar which can be accessed by various

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