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regenerate html pages with new txt2rst tool

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Axel Kohlmeyer 2016-09-07 10:09:53 -04:00
parent 44ce6fac4b
commit 5feedbd829
319 changed files with 4360 additions and 4585 deletions
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4
doc/html/Section_accelerate.html
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@ -346,8 +346,8 @@ package and are explained in the individual accelerator doc pages,
listed above:</p> listed above:</p>
<table border="1" class="docutils"> <table border="1" class="docutils">
<colgroup> <colgroup>
<col width="65%" /> <col width="64%" />
<col width="35%" /> <col width="36%" />
</colgroup> </colgroup>
<tbody valign="top"> <tbody valign="top">
<tr class="row-odd"><td>build the accelerator library</td> <tr class="row-odd"><td>build the accelerator library</td>

12
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 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 to use numeric formulas in an input script without having to assign
them to variable names. For example, these 3 input script lines:</p> them to variable names. For example, these 3 input script lines:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span>variable X equal (xlo+xhi)/2+sqrt(v_area) <pre class="literal-block">
variable X equal (xlo+xhi)/2+sqrt(v_area)
region 1 block $X 2 INF INF EDGE EDGE region 1 block $X 2 INF INF EDGE EDGE
variable X delete variable X delete
</pre></div> </pre>
</div>
<p>can be replaced by</p> <p>can be replaced by</p>
<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 class="literal-block">
</pre></div> region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE
</div> </pre>
<p>so that you do not have to define (or discard) a temporary variable X.</p> <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 <p>Note that neither the curly-bracket or immediate form of variables can
contain nested $ characters for other variables to substitute for. contain nested $ characters for other variables to substitute for.

10
doc/html/Section_errors.html
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@ -486,7 +486,7 @@ be computed.</dd>
<dt><em>Bad TIP4P bond type for PPPMDisp/TIP4P</em></dt> <dt><em>Bad TIP4P bond type for PPPMDisp/TIP4P</em></dt>
<dd>Specified bond type is not valid.</dd> <dd>Specified bond type is not valid.</dd>
<dt><em>Bad fix ID in fix append/atoms command</em></dt> <dt><em>Bad fix ID in fix append/atoms command</em></dt>
<dd>The value of the fix_id for keyword spatial must start with &#8216;<a href="#id6"><span class="problematic" id="id7">f_</span></a>&#8216;.</dd> <dd>The value of the fix_id for keyword spatial must start with &#8216;f_&#8217;.</dd>
<dt><em>Bad grid of processors</em></dt> <dt><em>Bad grid of processors</em></dt>
<dd>The 3d grid of processors defined by the processors command does not <dd>The 3d grid of processors defined by the processors command does not
match the number of processors LAMMPS is being run on.</dd> match the number of processors LAMMPS is being run on.</dd>
@ -6358,13 +6358,13 @@ have an infinite periodic crystal with bonds then it is impossible to
have fully consistent image flags, since some bonds will cross have fully consistent image flags, since some bonds will cross
periodic boundaries and connect two atoms with the same image periodic boundaries and connect two atoms with the same image
flag.</dd> flag.</dd>
<dt><em>KIM Model does not provide `energy&#8217;; Potential energy will be zero</em></dt> <dt><em>KIM Model does not provide &#8216;energy&#8217;; Potential energy will be zero</em></dt>
<dd>Self-explanatory.</dd> <dd>Self-explanatory.</dd>
<dt><em>KIM Model does not provide `forces&#8217;; Forces will be zero</em></dt> <dt><em>KIM Model does not provide &#8216;forces&#8217;; Forces will be zero</em></dt>
<dd>Self-explanatory.</dd> <dd>Self-explanatory.</dd>
<dt><em>KIM Model does not provide `particleEnergy&#8217;; energy per atom will be zero</em></dt> <dt><em>KIM Model does not provide &#8216;particleEnergy&#8217;; energy per atom will be zero</em></dt>
<dd>Self-explanatory.</dd> <dd>Self-explanatory.</dd>
<dt><em>KIM Model does not provide `particleVirial&#8217;; virial per atom will be zero</em></dt> <dt><em>KIM Model does not provide &#8216;particleVirial&#8217;; virial per atom will be zero</em></dt>
<dd>Self-explanatory.</dd> <dd>Self-explanatory.</dd>
<dt><em>Kspace_modify slab param &lt; 2.0 may cause unphysical behavior</em></dt> <dt><em>Kspace_modify slab param &lt; 2.0 may cause unphysical behavior</em></dt>
<dd>The kspace_modify slab parameter should be larger to insure periodic <dd>The kspace_modify slab parameter should be larger to insure periodic

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> </tbody>
</table> </table>
<p>Here is how you can run and visualize one of the sample problems:</p> <p>Here is how you can run and visualize one of the sample problems:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">cd</span> <span class="n">indent</span> <pre class="literal-block">
<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> cd indent
<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> cp ../../src/lmp_linux . # copy LAMMPS executable to this dir
</pre></div> lmp_linux -in in.indent # run the problem
</div> </pre>
<p>Running the simulation produces the files <em>dump.indent</em> and <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 <em>log.lammps</em>. You can visualize the dump file of snapshots with a
variety of 3rd-party tools highlighted on the 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 <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 Imagemagick command would create a GIF file suitable for viewing in a
browser.</p> browser.</p>
<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 class="literal-block">
</pre></div> % convert -loop 1 *.jpg foo.gif
</div> </pre>
</div> </div>
<hr class="docutils" /> <hr class="docutils" />
<div class="section" id="uppercase-directories"> <div class="section" id="uppercase-directories">
<h2>7.2. Uppercase directories</h2> <h2>7.2. Uppercase directories</h2>
<table border="1" class="docutils"> <table border="1" class="docutils">
<colgroup> <colgroup>
<col width="10%" /> <col width="11%" />
<col width="90%" /> <col width="89%" />
</colgroup> </colgroup>
<tbody valign="top"> <tbody valign="top">
<tr class="row-odd"><td>ASPHERE</td> <tr class="row-odd"><td>ASPHERE</td>

316
doc/html/Section_howto.html
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@ -252,13 +252,13 @@ scripts are based on. If that script had the line</p>
and tmp.restart.100) as it ran.</p> and tmp.restart.100) as it ran.</p>
<p>This script could be used to read the 1st restart file and re-run the <p>This script could be used to read the 1st restart file and re-run the
last 50 timesteps:</p> last 50 timesteps:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">read_restart</span> <span class="n">tmp</span><span class="o">.</span><span class="n">restart</span><span class="o">.</span><span class="mi">50</span> <pre class="literal-block">
</pre></div> read_restart tmp.restart.50
</div> </pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">neighbor</span> <span class="mf">0.4</span> <span class="nb">bin</span> <pre class="literal-block">
<span class="n">neigh_modify</span> <span class="n">every</span> <span class="mi">1</span> <span class="n">delay</span> <span class="mi">1</span> neighbor 0.4 bin
</pre></div> neigh_modify every 1 delay 1
</div> </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> <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">2</span> <span class="nb">all</span> <span class="n">langevin</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">10.0</span> <span class="mi">904297</span> <span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">langevin</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">10.0</span> <span class="mi">904297</span>
</pre></div> </pre></div>
@ -281,25 +281,25 @@ notice that the thermodynamic data match at step 50 (if you also put a
uses random numbers in a way that does not allow for perfect restarts.</p> uses random numbers in a way that does not allow for perfect restarts.</p>
<p>As an alternate approach, the restart file could be converted to a data <p>As an alternate approach, the restart file could be converted to a data
file as follows:</p> file as follows:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_g</span><span class="o">++</span> <span class="o">-</span><span class="n">r</span> <span class="n">tmp</span><span class="o">.</span><span class="n">restart</span><span class="o">.</span><span class="mi">50</span> <span class="n">tmp</span><span class="o">.</span><span class="n">restart</span><span class="o">.</span><span class="n">data</span> <pre class="literal-block">
</pre></div> lmp_g++ -r tmp.restart.50 tmp.restart.data
</div> </pre>
<p>Then, this script could be used to re-run the last 50 steps:</p> <p>Then, this script could be used to re-run the last 50 steps:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">units</span> <span class="n">lj</span> <pre class="literal-block">
<span class="n">atom_style</span> <span class="n">bond</span> units lj
<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="mf">1.12</span> atom_style bond
<span class="n">pair_modify</span> <span class="n">shift</span> <span class="n">yes</span> pair_style lj/cut 1.12
<span class="n">bond_style</span> <span class="n">fene</span> pair_modify shift yes
<span class="n">special_bonds</span> <span class="mf">0.0</span> <span class="mf">1.0</span> <span class="mf">1.0</span> bond_style fene
</pre></div> special_bonds 0.0 1.0 1.0
</div> </pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">read_data</span> <span class="n">tmp</span><span class="o">.</span><span class="n">restart</span><span class="o">.</span><span class="n">data</span> <pre class="literal-block">
</pre></div> read_data tmp.restart.data
</div> </pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">neighbor</span> <span class="mf">0.4</span> <span class="nb">bin</span> <pre class="literal-block">
<span class="n">neigh_modify</span> <span class="n">every</span> <span class="mi">1</span> <span class="n">delay</span> <span class="mi">1</span> neighbor 0.4 bin
</pre></div> neigh_modify every 1 delay 1
</div> </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> <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">2</span> <span class="nb">all</span> <span class="n">langevin</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">10.0</span> <span class="mi">904297</span> <span class="n">fix</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">langevin</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">10.0</span> <span class="mi">904297</span>
</pre></div> </pre></div>
@ -307,10 +307,10 @@ file as follows:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">timestep</span> <span class="mf">0.012</span> <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">timestep</span> <span class="mf">0.012</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">reset_timestep</span> <span class="mi">50</span> <pre class="literal-block">
<span class="n">run</span> <span class="mi">50</span> reset_timestep 50
</pre></div> run 50
</div> </pre>
<p>Note that nearly all the settings specified in the original <em>in.chain</em> <p>Note that nearly all the settings specified in the original <em>in.chain</em>
script must be repeated, except the <em>pair_coeff</em> and <em>bond_coeff</em> script must be repeated, except the <em>pair_coeff</em> and <em>bond_coeff</em>
commands since the new data file lists the force field coefficients. commands since the new data file lists the force field coefficients.
@ -420,39 +420,40 @@ individual commands for more details on how these examples work.</p>
<p>If &#8220;multiple simulations&#8221; means continue a previous simulation for <p>If &#8220;multiple simulations&#8221; means continue a previous simulation for
more timesteps, then you simply use the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command more timesteps, then you simply use the <a class="reference internal" href="run.html"><span class="doc">run</span></a> command
multiple times. For example, this script</p> multiple times. For example, this script</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">units</span> <span class="n">lj</span> <pre class="literal-block">
<span class="n">atom_style</span> <span class="n">atomic</span> units lj
<span class="n">read_data</span> <span class="n">data</span><span class="o">.</span><span class="n">lj</span> atom_style atomic
<span class="n">run</span> <span class="mi">10000</span> read_data data.lj
<span class="n">run</span> <span class="mi">10000</span> run 10000
<span class="n">run</span> <span class="mi">10000</span> run 10000
<span class="n">run</span> <span class="mi">10000</span> run 10000
<span class="n">run</span> <span class="mi">10000</span> run 10000
</pre></div> run 10000
</div> </pre>
<p>would run 5 successive simulations of the same system for a total of <p>would run 5 successive simulations of the same system for a total of
50,000 timesteps.</p> 50,000 timesteps.</p>
<p>If you wish to run totally different simulations, one after the other, <p>If you wish to run totally different simulations, one after the other,
the <a class="reference internal" href="clear.html"><span class="doc">clear</span></a> command can be used in between them to the <a class="reference internal" href="clear.html"><span class="doc">clear</span></a> command can be used in between them to
re-initialize LAMMPS. For example, this script</p> re-initialize LAMMPS. For example, this script</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">units</span> <span class="n">lj</span> <pre class="literal-block">
<span class="n">atom_style</span> <span class="n">atomic</span> units lj
<span class="n">read_data</span> <span class="n">data</span><span class="o">.</span><span class="n">lj</span> atom_style atomic
<span class="n">run</span> <span class="mi">10000</span> read_data data.lj
<span class="n">clear</span> run 10000
<span class="n">units</span> <span class="n">lj</span> clear
<span class="n">atom_style</span> <span class="n">atomic</span> units lj
<span class="n">read_data</span> <span class="n">data</span><span class="o">.</span><span class="n">lj</span><span class="o">.</span><span class="n">new</span> atom_style atomic
<span class="n">run</span> <span class="mi">10000</span> read_data data.lj.new
</pre></div> run 10000
</div> </pre>
<p>would run 2 independent simulations, one after the other.</p> <p>would run 2 independent simulations, one after the other.</p>
<p>For large numbers of independent simulations, you can use <p>For large numbers of independent simulations, you can use
<a class="reference internal" href="variable.html"><span class="doc">variables</span></a> and the <a class="reference internal" href="next.html"><span class="doc">next</span></a> and <a class="reference internal" href="variable.html"><span class="doc">variables</span></a> and the <a class="reference internal" href="next.html"><span class="doc">next</span></a> and
<a class="reference internal" href="jump.html"><span class="doc">jump</span></a> commands to loop over the same input script <a class="reference internal" href="jump.html"><span class="doc">jump</span></a> commands to loop over the same input script
multiple times with different settings. For example, this multiple times with different settings. For example, this
script, named in.polymer</p> script, named in.polymer</p>
<div class="highlight-default"><div class="highlight"><pre><span></span>variable d index run1 run2 run3 run4 run5 run6 run7 run8 <pre class="literal-block">
variable d index run1 run2 run3 run4 run5 run6 run7 run8
shell cd $d shell cd $d
read_data data.polymer read_data data.polymer
run 10000 run 10000
@ -460,8 +461,7 @@ shell cd ..
clear clear
next d next d
jump in.polymer jump in.polymer
</pre></div> </pre>
</div>
<p>would run 8 simulations in different directories, using a data.polymer <p>would run 8 simulations in different directories, using a data.polymer
file in each directory. The same concept could be used to run the file in each directory. The same concept could be used to run the
same system at 8 different temperatures, using a temperature variable same system at 8 different temperatures, using a temperature variable
@ -528,10 +528,10 @@ replica. The processors assigned to each replica are determined at
run-time by using the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-partition command-line switch</span></a> to launch LAMMPS on multiple run-time by using the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-partition command-line switch</span></a> to launch LAMMPS on multiple
partitions, which in this context are the same as replicas. E.g. partitions, which in this context are the same as replicas. E.g.
these commands:</p> these commands:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">16</span> <span class="n">lmp_linux</span> <span class="o">-</span><span class="n">partition</span> <span class="mi">8</span><span class="n">x2</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">temper</span> <pre class="literal-block">
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">8</span> <span class="n">lmp_linux</span> <span class="o">-</span><span class="n">partition</span> <span class="mi">8</span><span class="n">x1</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">neb</span> mpirun -np 16 lmp_linux -partition 8x2 -in in.temper
</pre></div> mpirun -np 8 lmp_linux -partition 8x1 -in in.neb
</div> </pre>
<p>would each run 8 replicas, on either 16 or 8 processors. Note the use <p>would each run 8 replicas, on either 16 or 8 processors. Note the use
of the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-in command-line switch</span></a> to specify of the <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">-in command-line switch</span></a> to specify
the input script which is required when running in multi-replica mode.</p> the input script which is required when running in multi-replica mode.</p>
@ -933,7 +933,7 @@ vectors of a general parallelepiped, where there is no restriction on
<strong>A</strong> x <strong>B</strong> . <strong>C</strong> &gt; 0. The equivalent LAMMPS <strong>a</strong>,<strong>b</strong>,<strong>c</strong> are a linear <strong>A</strong> x <strong>B</strong> . <strong>C</strong> &gt; 0. The equivalent LAMMPS <strong>a</strong>,<strong>b</strong>,<strong>c</strong> are a linear
rotation of <strong>A</strong>, <strong>B</strong>, and <strong>C</strong> and can be computed as follows:</p> rotation of <strong>A</strong>, <strong>B</strong>, and <strong>C</strong> and can be computed as follows:</p>
<img alt="_images/transform.jpg" class="align-center" src="_images/transform.jpg" /> <img alt="_images/transform.jpg" class="align-center" src="_images/transform.jpg" />
<p>where A = <a href="#id3"><span class="problematic" id="id4">|</span></a><strong>A</strong>| indicates the scalar length of <strong>A</strong>. The hat symbol <p>where A = | <strong>A</strong> | indicates the scalar length of <strong>A</strong>. The hat symbol (^)
indicates the corresponding unit vector. <em>beta</em> and <em>gamma</em> are angles indicates the corresponding unit vector. <em>beta</em> and <em>gamma</em> are angles
between the vectors described below. Note that by construction, between the vectors described below. Note that by construction,
<strong>a</strong>, <strong>b</strong>, and <strong>c</strong> have strictly positive x, y, and z components, respectively. <strong>a</strong>, <strong>b</strong>, and <strong>c</strong> have strictly positive x, y, and z components, respectively.
@ -1037,23 +1037,23 @@ BOUNDS for a snapshot is written to a dump file for a triclinic box,
an orthogonal bounding box which encloses the triclinic simulation box an orthogonal bounding box which encloses the triclinic simulation box
is output, along with the 3 tilt factors (xy, xz, yz) of the triclinic is output, along with the 3 tilt factors (xy, xz, yz) of the triclinic
box, formatted as follows:</p> box, formatted as follows:</p>
<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> <pre class="literal-block">
<span class="n">xlo_bound</span> <span class="n">xhi_bound</span> <span class="n">xy</span> ITEM: BOX BOUNDS xy xz yz
<span class="n">ylo_bound</span> <span class="n">yhi_bound</span> <span class="n">xz</span> xlo_bound xhi_bound xy
<span class="n">zlo_bound</span> <span class="n">zhi_bound</span> <span class="n">yz</span> ylo_bound yhi_bound xz
</pre></div> zlo_bound zhi_bound yz
</div> </pre>
<p>This bounding box is convenient for many visualization programs and is <p>This bounding box is convenient for many visualization programs and is
calculated from the 9 triclinic box parameters calculated from the 9 triclinic box parameters
(xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) as follows:</p> (xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz) as follows:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">xlo_bound</span> <span class="o">=</span> <span class="n">xlo</span> <span class="o">+</span> <span class="n">MIN</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span><span class="n">xy</span><span class="p">,</span><span class="n">xz</span><span class="p">,</span><span class="n">xy</span><span class="o">+</span><span class="n">xz</span><span class="p">)</span> <pre class="literal-block">
<span class="n">xhi_bound</span> <span class="o">=</span> <span class="n">xhi</span> <span class="o">+</span> <span class="n">MAX</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span><span class="n">xy</span><span class="p">,</span><span class="n">xz</span><span class="p">,</span><span class="n">xy</span><span class="o">+</span><span class="n">xz</span><span class="p">)</span> xlo_bound = xlo + MIN(0.0,xy,xz,xy+xz)
<span class="n">ylo_bound</span> <span class="o">=</span> <span class="n">ylo</span> <span class="o">+</span> <span class="n">MIN</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span><span class="n">yz</span><span class="p">)</span> xhi_bound = xhi + MAX(0.0,xy,xz,xy+xz)
<span class="n">yhi_bound</span> <span class="o">=</span> <span class="n">yhi</span> <span class="o">+</span> <span class="n">MAX</span><span class="p">(</span><span class="mf">0.0</span><span class="p">,</span><span class="n">yz</span><span class="p">)</span> ylo_bound = ylo + MIN(0.0,yz)
<span class="n">zlo_bound</span> <span class="o">=</span> <span class="n">zlo</span> yhi_bound = yhi + MAX(0.0,yz)
<span class="n">zhi_bound</span> <span class="o">=</span> <span class="n">zhi</span> zlo_bound = zlo
</pre></div> zhi_bound = zhi
</div> </pre>
<p>These formulas can be inverted if you need to convert the bounding box <p>These formulas can be inverted if you need to convert the bounding box
back into the triclinic box parameters, e.g. xlo = xlo_bound - back into the triclinic box parameters, e.g. xlo = xlo_bound -
MIN(0.0,xy,xz,xy+xz).</p> MIN(0.0,xy,xz,xy+xz).</p>
@ -1136,9 +1136,9 @@ of individual particles, after then are created.</p>
<p>The dipole style does not actually define finite-size particles, but <p>The dipole style does not actually define finite-size particles, but
is often used in conjunction with spherical particles, via a command is often used in conjunction with spherical particles, via a command
like</p> like</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_style</span> <span class="n">hybrid</span> <span class="n">sphere</span> <span class="n">dipole</span> <pre class="literal-block">
</pre></div> atom_style hybrid sphere dipole
</div> </pre>
<p>This is because when dipoles interact with each other, they induce <p>This is because when dipoles interact with each other, they induce
torques, and a particle must be finite-size (i.e. have a moment of torques, and a particle must be finite-size (i.e. have a moment of
inertia) in order to respond and rotate. See the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style dipole</span></a> command for details. The &#8220;set&#8221; command can be inertia) in order to respond and rotate. See the <a class="reference internal" href="atom_style.html"><span class="doc">atom_style dipole</span></a> command for details. The &#8220;set&#8221; command can be
@ -1372,11 +1372,11 @@ per-atom vector.</p>
<p>When a quantity is accessed, as in many of the output commands <p>When a quantity is accessed, as in many of the output commands
discussed below, it can be referenced via the following bracket discussed below, it can be referenced via the following bracket
notation, where ID in this case is the ID of a compute. The leading notation, where ID in this case is the ID of a compute. The leading
&#8220;<a href="#id74"><span class="problematic" id="id75">c_</span></a>&#8221; would be replaced by &#8220;<a href="#id76"><span class="problematic" id="id77">f_</span></a>&#8221; for a fix, or &#8220;<a href="#id78"><span class="problematic" id="id79">v_</span></a>&#8221; for a variable:</p> &#8220;c_&#8221; would be replaced by &#8220;f_&#8221; for a fix, or &#8220;v_&#8221; for a variable:</p>
<table border="1" class="docutils"> <table border="1" class="docutils">
<colgroup> <colgroup>
<col width="21%" /> <col width="23%" />
<col width="79%" /> <col width="77%" />
</colgroup> </colgroup>
<tbody valign="top"> <tbody valign="top">
<tr class="row-odd"><td>c_ID</td> <tr class="row-odd"><td>c_ID</td>
@ -1911,13 +1911,13 @@ internal LAMMPS operations. Note that LAMMPS classes are defined
within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++ within a LAMMPS namespace (LAMMPS_NS) if you use them from another C++
application.</p> application.</p>
<p>Library.cpp contains these 5 basic functions:</p> <p>Library.cpp contains these 5 basic functions:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">void</span> <span class="n">lammps_open</span><span class="p">(</span><span class="nb">int</span><span class="p">,</span> <span class="n">char</span> <span class="o">**</span><span class="p">,</span> <span class="n">MPI_Comm</span><span class="p">,</span> <span class="n">void</span> <span class="o">**</span><span class="p">)</span> <pre class="literal-block">
<span class="n">void</span> <span class="n">lammps_close</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">)</span> void lammps_open(int, char **, MPI_Comm, void **)
<span class="nb">int</span> <span class="n">lammps_version</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">)</span> void lammps_close(void *)
<span class="n">void</span> <span class="n">lammps_file</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">,</span> <span class="n">char</span> <span class="o">*</span><span class="p">)</span> int lammps_version(void *)
<span class="n">char</span> <span class="o">*</span><span class="n">lammps_command</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">,</span> <span class="n">char</span> <span class="o">*</span><span class="p">)</span> void lammps_file(void *, char *)
</pre></div> char *lammps_command(void *, char *)
</div> </pre>
<p>The lammps_open() function is used to initialize LAMMPS, passing in a <p>The lammps_open() function is used to initialize LAMMPS, passing in a
list of strings as if they were <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line arguments</span></a> when LAMMPS is run in list of strings as if they were <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line arguments</span></a> when LAMMPS is run in
stand-alone mode from the command line, and a MPI communicator for stand-alone mode from the command line, and a MPI communicator for
@ -1951,17 +1951,17 @@ interleaving the lammps_command() calls with other calls to extract
information from LAMMPS, perform its own operations, or call another information from LAMMPS, perform its own operations, or call another
code&#8217;s library.</p> code&#8217;s library.</p>
<p>Other useful functions are also included in library.cpp. For example:</p> <p>Other useful functions are also included in library.cpp. For example:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">void</span> <span class="o">*</span><span class="n">lammps_extract_global</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">,</span> <span class="n">char</span> <span class="o">*</span><span class="p">)</span> <pre class="literal-block">
<span class="n">void</span> <span class="o">*</span><span class="n">lammps_extract_atom</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">,</span> <span class="n">char</span> <span class="o">*</span><span class="p">)</span> void *lammps_extract_global(void *, char *)
<span class="n">void</span> <span class="o">*</span><span class="n">lammps_extract_compute</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">,</span> <span class="n">char</span> <span class="o">*</span><span class="p">,</span> <span class="nb">int</span><span class="p">,</span> <span class="nb">int</span><span class="p">)</span> void *lammps_extract_atom(void *, char *)
<span class="n">void</span> <span class="o">*</span><span class="n">lammps_extract_fix</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">,</span> <span class="n">char</span> <span class="o">*</span><span class="p">,</span> <span class="nb">int</span><span class="p">,</span> <span class="nb">int</span><span class="p">,</span> <span class="nb">int</span><span class="p">,</span> <span class="nb">int</span><span class="p">)</span> void *lammps_extract_compute(void *, char *, int, int)
<span class="n">void</span> <span class="o">*</span><span class="n">lammps_extract_variable</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">,</span> <span class="n">char</span> <span class="o">*</span><span class="p">,</span> <span class="n">char</span> <span class="o">*</span><span class="p">)</span> void *lammps_extract_fix(void *, char *, int, int, int, int)
<span class="nb">int</span> <span class="n">lammps_set_variable</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">,</span> <span class="n">char</span> <span class="o">*</span><span class="p">,</span> <span class="n">char</span> <span class="o">*</span><span class="p">)</span> void *lammps_extract_variable(void *, char *, char *)
<span class="nb">int</span> <span class="n">lammps_get_natoms</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">)</span> int lammps_set_variable(void *, char *, char *)
<span class="n">void</span> <span class="n">lammps_get_coords</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">,</span> <span class="n">double</span> <span class="o">*</span><span class="p">)</span> int lammps_get_natoms(void *)
<span class="n">void</span> <span class="n">lammps_put_coords</span><span class="p">(</span><span class="n">void</span> <span class="o">*</span><span class="p">,</span> <span class="n">double</span> <span class="o">*</span><span class="p">)</span> void lammps_get_coords(void *, double *)
</pre></div> void lammps_put_coords(void *, double *)
</div> </pre>
<p>These can extract various global or per-atom quantities from LAMMPS as <p>These can extract various global or per-atom quantities from LAMMPS as
well as values calculated by a compute, fix, or variable. The well as values calculated by a compute, fix, or variable. The
&#8220;set_variable&#8221; function can set an existing string-style variable to a &#8220;set_variable&#8221; function can set an existing string-style variable to a
@ -2087,29 +2087,30 @@ liquid Ar via the GK formalism:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Sample LAMMPS input script for viscosity of liquid Ar</span> <div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Sample LAMMPS input script for viscosity of liquid Ar</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span>units real <pre class="literal-block">
units real
variable T equal 86.4956 variable T equal 86.4956
variable V equal vol variable V equal vol
variable dt equal 4.0 variable dt equal 4.0
variable p equal 400 # correlation length variable p equal 400 # correlation length
variable s equal 5 # sample interval variable s equal 5 # sample interval
variable d equal $p*$s # dump interval variable d equal $p*$s # dump interval
</pre></div> </pre>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># convert from LAMMPS real units to SI</span> <div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># convert from LAMMPS real units to SI</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span>variable kB equal 1.3806504e-23 # [J/K/** Boltzmann <pre class="literal-block">
variable kB equal 1.3806504e-23 # [J/K/** Boltzmann
variable atm2Pa equal 101325.0 variable atm2Pa equal 101325.0
variable A2m equal 1.0e-10 variable A2m equal 1.0e-10
variable fs2s equal 1.0e-15 variable fs2s equal 1.0e-15
variable convert equal ${atm2Pa}*${atm2Pa}*${fs2s}*${A2m}*${A2m}*${A2m} variable convert equal ${atm2Pa}*${atm2Pa}*${fs2s}*${A2m}*${A2m}*${A2m}
</pre></div> </pre>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># setup problem</span> <div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># setup problem</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span>dimension 3 <pre class="literal-block">
dimension 3
boundary p p p boundary p p p
lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
region box block 0 4 0 4 0 4 region box block 0 4 0 4 0 4
@ -2120,8 +2121,7 @@ pair_style lj/cut 13.0
pair_coeff * * 0.2381 3.405 pair_coeff * * 0.2381 3.405
timestep ${dt} timestep ${dt}
thermo $d thermo $d
</pre></div> </pre>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># equilibration and thermalization</span> <div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># equilibration and thermalization</span>
</pre></div> </pre></div>
</div> </div>
@ -2137,7 +2137,8 @@ run 8000
<span class="c1">#fix NVE all nve</span> <span class="c1">#fix NVE all nve</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span>reset_timestep 0 <pre class="literal-block">
reset_timestep 0
variable pxy equal pxy variable pxy equal pxy
variable pxz equal pxz variable pxz equal pxz
variable pyz equal pyz variable pyz equal pyz
@ -2151,9 +2152,8 @@ thermo_style custom step temp press v_pxy v_pxz v_pyz v_v11 v_v22 v_v33
run 100000 run 100000
variable v equal (v_v11+v_v22+v_v33)/3.0 variable v equal (v_v11+v_v22+v_v33)/3.0
variable ndens equal count(all)/vol variable ndens equal count(all)/vol
print &quot;average viscosity: $v [Pa.s/** @ $T K, ${ndens} /A^3&quot; print &quot;average viscosity: $v [Pa.s/** &#64; $T K, ${ndens} /A^3&quot;
</pre></div> </pre>
</div>
<p>The fifth method is related to the above Green-Kubo method, <p>The fifth method is related to the above Green-Kubo method,
but uses the Einstein formulation, analogous to the Einstein but uses the Einstein formulation, analogous to the Einstein
mean-square-displacement formulation for self-diffusivity. The mean-square-displacement formulation for self-diffusivity. The
@ -2274,7 +2274,7 @@ fix produces a global array as output with one row of values per
chunk.</p> chunk.</p>
</div> </div>
<div class="section" id="compute-chunk-commands"> <div class="section" id="compute-chunk-commands">
<h3>6.23.3. Compute <a href="#id71"><span class="problematic" id="id72">*</span></a>/chunk commands:</h3> <h3>6.23.3. Compute */chunk commands:</h3>
<p>Currently the following computes operate on chunks of atoms to produce <p>Currently the following computes operate on chunks of atoms to produce
per-chunk values.</p> per-chunk values.</p>
<ul class="simple"> <ul class="simple">
@ -2331,31 +2331,31 @@ velocity:</p>
<ol class="arabic simple" start="3"> <ol class="arabic simple" start="3">
<li>Center of mass of each molecule:</li> <li>Center of mass of each molecule:</li>
</ol> </ol>
<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> <pre class="literal-block">
<span class="n">compute</span> <span class="n">myChunk</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> compute cc1 all chunk/atom molecule
<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> compute myChunk all com/chunk cc1
</pre></div> fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
</div> </pre>
<ol class="arabic simple" start="4"> <ol class="arabic simple" start="4">
<li>Total force on each molecule and ave/max across all molecules:</li> <li>Total force on each molecule and ave/max across all molecules:</li>
</ol> </ol>
<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> <pre class="literal-block">
<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">1000</span> <span class="mi">1</span> <span class="mi">1000</span> <span class="n">cc1</span> <span class="n">fx</span> <span class="n">fy</span> <span class="n">fz</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span> compute cc1 all chunk/atom molecule
<span class="n">variable</span> <span class="n">xave</span> <span class="n">equal</span> <span class="n">ave</span><span class="p">(</span><span class="n">f_1</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span> fix 1 all ave/chunk 1000 1 1000 cc1 fx fy fz file tmp.out
<span class="n">variable</span> <span class="n">xmax</span> <span class="n">equal</span> <span class="nb">max</span><span class="p">(</span><span class="n">f_1</span><span class="p">[</span><span class="mi">2</span><span class="p">])</span> variable xave equal ave(f_1[2])
<span class="n">thermo</span> <span class="mi">1000</span> variable xmax equal max(f_1[2])
<span class="n">thermo_style</span> <span class="n">custom</span> <span class="n">step</span> <span class="n">temp</span> <span class="n">v_xave</span> <span class="n">v_xmax</span> thermo 1000
</pre></div> thermo_style custom step temp v_xave v_xmax
</div> </pre>
<ol class="arabic simple" start="5"> <ol class="arabic simple" start="5">
<li>Histogram of cluster sizes:</li> <li>Histogram of cluster sizes:</li>
</ol> </ol>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">cluster</span> <span class="nb">all</span> <span class="n">cluster</span><span class="o">/</span><span class="n">atom</span> <span class="mf">1.0</span> <pre class="literal-block">
<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">c_cluster</span> <span class="n">compress</span> <span class="n">yes</span> compute cluster all cluster/atom 1.0
<span class="n">compute</span> <span class="n">size</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> compute cc1 all chunk/atom c_cluster compress yes
<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="mi">0</span> <span class="mi">20</span> <span class="mi">20</span> <span class="n">c_size</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">ignore</span> <span class="n">file</span> <span class="n">tmp</span><span class="o">.</span><span class="n">histo</span> compute size all property/chunk cc1 count
</pre></div> fix 1 all ave/histo 100 1 100 0 20 20 c_size mode vector ave running beyond ignore file tmp.histo
</div> </pre>
<hr class="docutils" /> <hr class="docutils" />
</div> </div>
</div> </div>
@ -2607,18 +2607,18 @@ by the <a class="reference internal" href="kspace_style.html"><span class="doc">
Ewald solvers can be used.</p> Ewald solvers can be used.</p>
<p>For the NaCL example problem, these pair style and bond style settings <p>For the NaCL example problem, these pair style and bond style settings
are used:</p> are used:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">born</span><span class="o">/</span><span class="n">coul</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">cs</span> <span class="mf">20.0</span> <span class="mf">20.0</span> <pre class="literal-block">
<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">0.0</span> <span class="mf">1.000</span> <span class="mf">0.00</span> <span class="mf">0.00</span> <span class="mf">0.00</span> pair_style born/coul/long/cs 20.0 20.0
<span class="n">pair_coeff</span> <span class="mi">3</span> <span class="mi">3</span> <span class="mf">487.0</span> <span class="mf">0.23768</span> <span class="mf">0.00</span> <span class="mf">1.05</span> <span class="mf">0.50</span> <span class="c1">#Na-Na</span> pair_coeff * * 0.0 1.000 0.00 0.00 0.00
<span class="n">pair_coeff</span> <span class="mi">3</span> <span class="mi">4</span> <span class="mf">145134.0</span> <span class="mf">0.23768</span> <span class="mf">0.00</span> <span class="mf">6.99</span> <span class="mf">8.70</span> <span class="c1">#Na-Cl</span> pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na
<span class="n">pair_coeff</span> <span class="mi">4</span> <span class="mi">4</span> <span class="mf">405774.0</span> <span class="mf">0.23768</span> <span class="mf">0.00</span> <span class="mf">72.40</span> <span class="mf">145.40</span> <span class="c1">#Cl-Cl</span> pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl
</pre></div> pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl
</div> </pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</span> <pre class="literal-block">
<span class="n">bond_coeff</span> <span class="mi">1</span> <span class="mf">63.014</span> <span class="mf">0.0</span> bond_style harmonic
<span class="n">bond_coeff</span> <span class="mi">2</span> <span class="mf">25.724</span> <span class="mf">0.0</span> bond_coeff 1 63.014 0.0
</pre></div> bond_coeff 2 25.724 0.0
</div> </pre>
<p>When running dynamics with the adiabatic core/shell model, the <p>When running dynamics with the adiabatic core/shell model, the
following issues should be considered. Since the relative motion of following issues should be considered. Since the relative motion of
the core and shell particles corresponds to the polarization, typical the core and shell particles corresponds to the polarization, typical
@ -2645,15 +2645,15 @@ used to assign the compute to the thermostat fix. Likewise the
<a class="reference internal" href="thermo_modify.html"><span class="doc">thermo_modify temp</span></a> command can be used to make <a class="reference internal" href="thermo_modify.html"><span class="doc">thermo_modify temp</span></a> command can be used to make
this temperature be output for the overall system.</p> this temperature be output for the overall system.</p>
<p>For the NaCl example, this can be done as follows:</p> <p>For the NaCl example, this can be done as follows:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">group</span> <span class="n">cores</span> <span class="nb">type</span> <span class="mi">1</span> <span class="mi">2</span> <pre class="literal-block">
<span class="n">group</span> <span class="n">shells</span> <span class="nb">type</span> <span class="mi">3</span> <span class="mi">4</span> group cores type 1 2
<span class="n">compute</span> <span class="n">CSequ</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> group shells type 3 4
<span class="n">fix</span> <span class="n">thermoberendsen</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">berendsen</span> <span class="mi">1427</span> <span class="mi">1427</span> <span class="mf">0.4</span> <span class="c1"># thermostat for the true physical system</span> compute CSequ all temp/cs cores shells
<span class="n">fix</span> <span class="n">thermostatequ</span> <span class="nb">all</span> <span class="n">nve</span> <span class="c1"># integrator as needed for the berendsen thermostat</span> fix thermoberendsen all temp/berendsen 1427 1427 0.4 # thermostat for the true physical system
<span class="n">fix_modify</span> <span class="n">thermoberendsen</span> <span class="n">temp</span> <span class="n">CSequ</span> fix thermostatequ all nve # integrator as needed for the berendsen thermostat
<span class="n">thermo_modify</span> <span class="n">temp</span> <span class="n">CSequ</span> <span class="c1"># output of center-of-mass derived temperature</span> fix_modify thermoberendsen temp CSequ
</pre></div> thermo_modify temp CSequ # output of center-of-mass derived temperature
</div> </pre>
<p>If <a class="reference internal" href="compute_temp_cs.html"><span class="doc">compute temp/cs</span></a> is used, the decoupled <p>If <a class="reference internal" href="compute_temp_cs.html"><span class="doc">compute temp/cs</span></a> is used, the decoupled
relative motion of the core and the shell should in theory be relative motion of the core and the shell should in theory be
stable. However numerical fluctuation can introduce a small stable. However numerical fluctuation can introduce a small
@ -2702,14 +2702,14 @@ accessed by the <a class="reference internal" href="compute_property_atom.html">
command, to use as input to the <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command to define the core/shell command, to use as input to the <a class="reference internal" href="compute_chunk_atom.html"><span class="doc">compute chunk/atom</span></a> command to define the core/shell
pairs as chunks.</p> pairs as chunks.</p>
<p>For example,</p> <p>For example,</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">csinfo</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">atom</span> <span class="n">i_CSID</span> <span class="c1"># property/atom command</span> <pre class="literal-block">
<span class="n">read_data</span> <span class="n">NaCl_CS_x0</span><span class="o">.</span><span class="mi">1</span><span class="n">_prop</span><span class="o">.</span><span class="n">data</span> <span class="n">fix</span> <span class="n">csinfo</span> <span class="n">NULL</span> <span class="n">CS</span><span class="o">-</span><span class="n">Info</span> <span class="c1"># atom property added in the data-file</span> fix csinfo all property/atom i_CSID # property/atom command
<span class="n">compute</span> <span class="n">prop</span> <span class="nb">all</span> <span class="nb">property</span><span class="o">/</span><span class="n">atom</span> <span class="n">i_CSID</span> read_data NaCl_CS_x0.1_prop.data fix csinfo NULL CS-Info # atom property added in the data-file
<span class="n">compute</span> <span class="n">cs_chunk</span> <span class="nb">all</span> <span class="n">chunk</span><span class="o">/</span><span class="n">atom</span> <span class="n">c_prop</span> compute prop all property/atom i_CSID
<span class="n">compute</span> <span class="n">cstherm</span> <span class="nb">all</span> <span class="n">temp</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cs_chunk</span> <span class="n">temp</span> <span class="n">internal</span> <span class="n">com</span> <span class="n">yes</span> <span class="n">cdof</span> <span class="mf">3.0</span> <span class="c1"># note the chosen degrees of freedom for the core/shell pairs</span> compute cs_chunk all chunk/atom c_prop
<span class="n">fix</span> <span class="n">ave_chunk</span> <span class="nb">all</span> <span class="n">ave</span><span class="o">/</span><span class="n">time</span> <span class="mi">10</span> <span class="mi">1</span> <span class="mi">10</span> <span class="n">c_cstherm</span> <span class="n">file</span> <span class="n">chunk</span><span class="o">.</span><span class="n">dump</span> <span class="n">mode</span> <span class="n">vector</span> compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 # note the chosen degrees of freedom for the core/shell pairs
</pre></div> fix ave_chunk all ave/time 10 1 10 c_cstherm file chunk.dump mode vector
</div> </pre>
<p>The additional section in the date file would be formatted like this:</p> <p>The additional section in the date file would be formatted like this:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">CS</span><span class="o">-</span><span class="n">Info</span> <span class="c1"># header of additional section</span> <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">CS</span><span class="o">-</span><span class="n">Info</span> <span class="c1"># header of additional section</span>
</pre></div> </pre></div>

102
doc/html/Section_modify.html
View File

@ -193,8 +193,8 @@ C-style data structures (vectors and arrays).</p>
<p>Most of the new features described in this section require you to <p>Most of the new features described in this section require you to
write a new C++ derived class (except for exceptions described below, write a new C++ derived class (except for exceptions described below,
where you can make small edits to existing files). Creating a new where you can make small edits to existing files). Creating a new
class requires 2 files, a source code file (<em>.cpp) and a header file class requires 2 files, a source code file (*.cpp) and a header file
(</em>.h). The derived class must provide certain methods to work as a (*.h). The derived class must provide certain methods to work as a
new option. Depending on how different your new feature is compared new option. Depending on how different your new feature is compared
to existing features, you can either derive from the base class to existing features, you can either derive from the base class
itself, or from a derived class that already exists. Enabling LAMMPS itself, or from a derived class that already exists. Enabling LAMMPS
@ -209,19 +209,19 @@ and pair_foo.h that define a new class PairFoo that computes pairwise
potentials described in the classic 1997 <a class="reference internal" href="#foo"><span class="std std-ref">paper</span></a> by Foo, et al. potentials described in the classic 1997 <a class="reference internal" href="#foo"><span class="std std-ref">paper</span></a> by Foo, et al.
If you wish to invoke those potentials in a LAMMPS input script with a If you wish to invoke those potentials in a LAMMPS input script with a
command like</p> command like</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">foo</span> <span class="mf">0.1</span> <span class="mf">3.5</span> <pre class="literal-block">
</pre></div> pair_style foo 0.1 3.5
</div> </pre>
<p>then your pair_foo.h file should be structured as follows:</p> <p>then your pair_foo.h file should be structured as follows:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1">#ifdef PAIR_CLASS</span> <pre class="literal-block">
<span class="n">PairStyle</span><span class="p">(</span><span class="n">foo</span><span class="p">,</span><span class="n">PairFoo</span><span class="p">)</span> #ifdef PAIR_CLASS
<span class="c1">#else</span> PairStyle(foo,PairFoo)
<span class="o">...</span> #else
<span class="p">(</span><span class="k">class</span> <span class="nc">definition</span> <span class="k">for</span> <span class="n">PairFoo</span><span class="p">)</span> ...
<span class="o">...</span> (class definition for PairFoo)
<span class="c1">#endif</span> ...
</pre></div> #endif
</div> </pre>
<p>where &#8220;foo&#8221; is the style keyword in the pair_style command, and <p>where &#8220;foo&#8221; is the style keyword in the pair_style command, and
PairFoo is the class name defined in your pair_foo.cpp and pair_foo.h PairFoo is the class name defined in your pair_foo.cpp and pair_foo.h
files.</p> files.</p>
@ -275,8 +275,8 @@ atoms.</p>
class. See atom_vec.h for details.</p> class. See atom_vec.h for details.</p>
<table border="1" class="docutils"> <table border="1" class="docutils">
<colgroup> <colgroup>
<col width="22%" /> <col width="24%" />
<col width="78%" /> <col width="76%" />
</colgroup> </colgroup>
<tbody valign="top"> <tbody valign="top">
<tr class="row-odd"><td>init</td> <tr class="row-odd"><td>init</td>
@ -393,18 +393,18 @@ output the custom values.</p>
The code for these classes can use the per-atom properties defined by The code for these classes can use the per-atom properties defined by
fix property/atom. The Atom class has a find_custom() method that is fix property/atom. The Atom class has a find_custom() method that is
useful in this context:</p> useful in this context:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="nb">int</span> <span class="n">index</span> <span class="o">=</span> <span class="n">atom</span><span class="o">-&gt;</span><span class="n">find_custom</span><span class="p">(</span><span class="n">char</span> <span class="o">*</span><span class="n">name</span><span class="p">,</span> <span class="nb">int</span> <span class="o">&amp;</span><span class="n">flag</span><span class="p">);</span> <pre class="literal-block">
</pre></div> int index = atom-&gt;find_custom(char *name, int &amp;flag);
</div> </pre>
<p>The &#8220;name&#8221; of a custom attribute, as specified in the <a class="reference internal" href="fix_property_atom.html"><span class="doc">fix property/atom</span></a> command, is checked to verify <p>The &#8220;name&#8221; of a custom attribute, as specified in the <a class="reference internal" href="fix_property_atom.html"><span class="doc">fix property/atom</span></a> command, is checked to verify
that it exists and its index is returned. The method also sets flag = that it exists and its index is returned. The method also sets flag =
0/1 depending on whether it is an integer or floating-point attribute. 0/1 depending on whether it is an integer or floating-point attribute.
The vector of values associated with the attribute can then be The vector of values associated with the attribute can then be
accessed using the returned index as</p> accessed using the returned index as</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="nb">int</span> <span class="o">*</span><span class="n">ivector</span> <span class="o">=</span> <span class="n">atom</span><span class="o">-&gt;</span><span class="n">ivector</span><span class="p">[</span><span class="n">index</span><span class="p">];</span> <pre class="literal-block">
<span class="n">double</span> <span class="o">*</span><span class="n">dvector</span> <span class="o">=</span> <span class="n">atom</span><span class="o">-&gt;</span><span class="n">dvector</span><span class="p">[</span><span class="n">index</span><span class="p">];</span> int *ivector = atom-&gt;ivector[index];
</pre></div> double *dvector = atom-&gt;dvector[index];
</div> </pre>
<p>Ivector or dvector are vectors of length Nlocal = # of owned atoms, <p>Ivector or dvector are vectors of length Nlocal = # of owned atoms,
which store the attributes of individual atoms.</p> which store the attributes of individual atoms.</p>
<hr class="docutils" /> <hr class="docutils" />
@ -474,8 +474,8 @@ per-atom kinetic energy.</p>
class. See compute.h for details.</p> class. See compute.h for details.</p>
<table border="1" class="docutils"> <table border="1" class="docutils">
<colgroup> <colgroup>
<col width="24%" /> <col width="26%" />
<col width="76%" /> <col width="74%" />
</colgroup> </colgroup>
<tbody valign="top"> <tbody valign="top">
<tr class="row-odd"><td>init</td> <tr class="row-odd"><td>init</td>
@ -551,8 +551,8 @@ DumpCustom class contained in the dump_custom.cpp file.</p>
class. See dump.h for details.</p> class. See dump.h for details.</p>
<table border="1" class="docutils"> <table border="1" class="docutils">
<colgroup> <colgroup>
<col width="22%" /> <col width="23%" />
<col width="78%" /> <col width="77%" />
</colgroup> </colgroup>
<tbody valign="top"> <tbody valign="top">
<tr class="row-odd"><td>write_header</td> <tr class="row-odd"><td>write_header</td>
@ -597,8 +597,8 @@ implement.</p>
derived class. See fix.h for details.</p> derived class. See fix.h for details.</p>
<table border="1" class="docutils"> <table border="1" class="docutils">
<colgroup> <colgroup>
<col width="22%" /> <col width="23%" />
<col width="78%" /> <col width="77%" />
</colgroup> </colgroup>
<tbody valign="top"> <tbody valign="top">
<tr class="row-odd"><td>setmask</td> <tr class="row-odd"><td>setmask</td>
@ -823,8 +823,8 @@ styles can be created to add new K-space options to LAMMPS.</p>
class. See kspace.h for details.</p> class. See kspace.h for details.</p>
<table border="1" class="docutils"> <table border="1" class="docutils">
<colgroup> <colgroup>
<col width="23%" /> <col width="25%" />
<col width="77%" /> <col width="75%" />
</colgroup> </colgroup>
<tbody valign="top"> <tbody valign="top">
<tr class="row-odd"><td>init</td> <tr class="row-odd"><td>init</td>
@ -853,8 +853,8 @@ LAMMPS.</p>
class. See min.h for details.</p> class. See min.h for details.</p>
<table border="1" class="docutils"> <table border="1" class="docutils">
<colgroup> <colgroup>
<col width="25%" /> <col width="26%" />
<col width="75%" /> <col width="74%" />
</colgroup> </colgroup>
<tbody valign="top"> <tbody valign="top">
<tr class="row-odd"><td>init</td> <tr class="row-odd"><td>init</td>
@ -882,8 +882,8 @@ includes some optional methods to enable its use with rRESPA.</p>
<p>Here is a brief description of the class methods in pair.h:</p> <p>Here is a brief description of the class methods in pair.h:</p>
<table border="1" class="docutils"> <table border="1" class="docutils">
<colgroup> <colgroup>
<col width="32%" /> <col width="33%" />
<col width="68%" /> <col width="67%" />
</colgroup> </colgroup>
<tbody valign="top"> <tbody valign="top">
<tr class="row-odd"><td>compute</td> <tr class="row-odd"><td>compute</td>
@ -929,8 +929,8 @@ styles can be created to add new region shapes to LAMMPS.</p>
class. See region.h for details.</p> class. See region.h for details.</p>
<table border="1" class="docutils"> <table border="1" class="docutils">
<colgroup> <colgroup>
<col width="21%" /> <col width="22%" />
<col width="79%" /> <col width="78%" />
</colgroup> </colgroup>
<tbody valign="top"> <tbody valign="top">
<tr class="row-odd"><td>inside</td> <tr class="row-odd"><td>inside</td>
@ -965,8 +965,8 @@ a rigid body containing N sub-particles.</p>
class. See body.h for details.</p> class. See body.h for details.</p>
<table border="1" class="docutils"> <table border="1" class="docutils">
<colgroup> <colgroup>
<col width="25%" /> <col width="27%" />
<col width="75%" /> <col width="73%" />
</colgroup> </colgroup>
<tbody valign="top"> <tbody valign="top">
<tr class="row-odd"><td>data_body</td> <tr class="row-odd"><td>data_body</td>
@ -1030,14 +1030,14 @@ via the <a class="reference internal" href="print.html"><span class="doc">print<
<a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style custom</span></a> commands. Variables of style <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style custom</span></a> commands. Variables of style
&#8220;equal&#8221; can compute complex equations that involve the following types &#8220;equal&#8221; can compute complex equations that involve the following types
of arguments:</p> of arguments:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">thermo</span> <span class="n">keywords</span> <span class="o">=</span> <span class="n">ke</span><span class="p">,</span> <span class="n">vol</span><span class="p">,</span> <span class="n">atoms</span><span class="p">,</span> <span class="o">...</span> <pre class="literal-block">
<span class="n">other</span> <span class="n">variables</span> <span class="o">=</span> <span class="n">v_a</span><span class="p">,</span> <span class="n">v_myvar</span><span class="p">,</span> <span class="o">...</span> thermo keywords = ke, vol, atoms, ...
<span class="n">math</span> <span class="n">functions</span> <span class="o">=</span> <span class="n">div</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">mult</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">add</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="o">...</span> other variables = v_a, v_myvar, ...
<span class="n">group</span> <span class="n">functions</span> <span class="o">=</span> <span class="n">mass</span><span class="p">(</span><span class="n">group</span><span class="p">),</span> <span class="n">xcm</span><span class="p">(</span><span class="n">group</span><span class="p">,</span><span class="n">x</span><span class="p">),</span> <span class="o">...</span> math functions = div(x,y), mult(x,y), add(x,y), ...
<span class="n">atom</span> <span class="n">values</span> <span class="o">=</span> <span class="n">x</span><span class="p">[</span><span class="mi">123</span><span class="p">],</span> <span class="n">y</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span> <span class="n">vx</span><span class="p">[</span><span class="mi">34</span><span class="p">],</span> <span class="o">...</span> group functions = mass(group), xcm(group,x), ...
<span class="n">compute</span> <span class="n">values</span> <span class="o">=</span> <span class="n">c_mytemp</span><span class="p">[</span><span class="mi">0</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">...</span> atom values = x[123], y[3], vx[34], ...
</pre></div> compute values = c_mytemp[0], c_thermo_press[3], ...
</div> </pre>
<p>Adding keywords for the <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style custom</span></a> command <p>Adding keywords for the <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style custom</span></a> command
(which can then be accessed by variables) was discussed (which can then be accessed by variables) was discussed
<a class="reference internal" href="Section_howto.html#thermo"><span class="std std-ref">here</span></a> on this page.</p> <a class="reference internal" href="Section_howto.html#thermo"><span class="std std-ref">here</span></a> on this page.</p>
@ -1157,7 +1157,7 @@ structures, performs its operations, and is formatted similar to other
LAMMPS source files, including the use of the error class for error LAMMPS source files, including the use of the error class for error
and warning messages.</li> and warning messages.</li>
<li>If you want your contribution to be added as a user-contributed <li>If you want your contribution to be added as a user-contributed
feature, and it&#8217;s a single file (actually a <a href="#id8"><span class="problematic" id="id9">*</span></a>.cpp and <a href="#id10"><span class="problematic" id="id11">*</span></a>.h file) it can feature, and it&#8217;s a single file (actually a *.cpp and *.h file) it can
rapidly be added to the USER-MISC directory. Send us the one-line rapidly be added to the USER-MISC directory. Send us the one-line
entry to add to the USER-MISC/README file in that dir, along with the entry to add to the USER-MISC/README file in that dir, along with the
2 source files. You can do this multiple times if you wish to 2 source files. You can do this multiple times if you wish to
@ -1192,12 +1192,12 @@ to HTML and PDF. The tools for this conversion are included in the
source distribution, and the translation can be as simple as doing source distribution, and the translation can be as simple as doing
&#8220;make html pdf&#8221; in the doc folder. &#8220;make html pdf&#8221; in the doc folder.
Thus the documentation source files must be in the same format and Thus the documentation source files must be in the same format and
style as other <em>.txt files in the lammps/doc/src directory for similar style as other *.txt files in the lammps/doc/src directory for similar
commands and styles; use one or more of them as a starting point. commands and styles; use one or more of them as a starting point.
A description of the markup can also be found in A description of the markup can also be found in
lammps/doc/utils/txt2html/README.html lammps/doc/utils/txt2html/README.html
As appropriate, the text files can include links to equations As appropriate, the text files can include links to equations
(see doc/Eqs/</em>.tex for examples, we auto-create the associated JPG (see doc/Eqs/*.tex for examples, we auto-create the associated JPG
files), or figures (see doc/JPG for examples), or even additional PDF files), or figures (see doc/JPG for examples), or even additional PDF
files with further details (see doc/PDF for examples). The doc page files with further details (see doc/PDF for examples). The doc page
should also include literature citations as appropriate; see the should also include literature citations as appropriate; see the
@ -1220,7 +1220,7 @@ These example inputs are also required for validating memory accesses
and testing for memory leaks with valgrind</li> and testing for memory leaks with valgrind</li>
<li>If there is a paper of yours describing your feature (either the <li>If there is a paper of yours describing your feature (either the
algorithm/science behind the feature itself, or its initial usage, or algorithm/science behind the feature itself, or its initial usage, or
its implementation in LAMMPS), you can add the citation to the <a href="#id12"><span class="problematic" id="id13">*</span></a>.cpp its implementation in LAMMPS), you can add the citation to the *.cpp
source file. See src/USER-EFF/atom_vec_electron.cpp for an example. source file. See src/USER-EFF/atom_vec_electron.cpp for an example.
A LaTeX citation is stored in a variable at the top of the file and a A LaTeX citation is stored in a variable at the top of the file and a
single line of code that references the variable is added to the single line of code that references the variable is added to the

257
doc/html/Section_packages.html
View File

@ -630,9 +630,9 @@ for aspherical particle models: ellipsoids, 2d lines, 3d triangles.</p>
<span class="n">make</span> <span class="n">machine</span> <span class="n">make</span> <span class="n">machine</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">asphere</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span> <pre class="literal-block">
</pre></div> Make.py -p ^asphere -a machine
</div> </pre>
<p>Supporting info: <a class="reference internal" href="Section_howto.html#howto-14"><span class="std std-ref">Section howto 6.14</span></a>, <p>Supporting info: <a class="reference internal" href="Section_howto.html#howto-14"><span class="std std-ref">Section howto 6.14</span></a>,
<a class="reference internal" href="pair_gayberne.html"><span class="doc">pair_style gayberne</span></a>, <a class="reference internal" href="pair_resquared.html"><span class="doc">pair_style resquared</span></a>, <a class="reference internal" href="pair_gayberne.html"><span class="doc">pair_style gayberne</span></a>, <a class="reference internal" href="pair_resquared.html"><span class="doc">pair_style resquared</span></a>,
<a class="reference external" href="PDF/pair_gayberne_extra.pdf">doc/PDF/pair_gayberne_extra.pdf</a>, <a class="reference external" href="PDF/pair_gayberne_extra.pdf">doc/PDF/pair_gayberne_extra.pdf</a>,
@ -658,9 +658,9 @@ themselves. See the <a class="reference internal" href="body.html"><span class=
<span class="n">make</span> <span class="n">machine</span> <span class="n">make</span> <span class="n">machine</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">body</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span> <pre class="literal-block">
</pre></div> Make.py -p ^body -a machine
</div> </pre>
<p>Supporting info: <a class="reference internal" href="atom_style.html"><span class="doc">atom_style body</span></a>, <a class="reference internal" href="body.html"><span class="doc">body</span></a>, <p>Supporting info: <a class="reference internal" href="atom_style.html"><span class="doc">atom_style body</span></a>, <a class="reference internal" href="body.html"><span class="doc">body</span></a>,
<a class="reference internal" href="pair_body.html"><span class="doc">pair_style body</span></a>, examples/body</p> <a class="reference internal" href="pair_body.html"><span class="doc">pair_style body</span></a>, examples/body</p>
<hr class="docutils" /> <hr class="docutils" />
@ -682,9 +682,9 @@ COMPASS CLASS2 molecular force field.</p>
<span class="n">make</span> <span class="n">machine</span> <span class="n">make</span> <span class="n">machine</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">class2</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span> <pre class="literal-block">
</pre></div> Make.py -p ^class2 -a machine
</div> </pre>
<p>Supporting info: <a class="reference internal" href="bond_class2.html"><span class="doc">bond_style class2</span></a>, <a class="reference internal" href="angle_class2.html"><span class="doc">angle_style class2</span></a>, <a class="reference internal" href="dihedral_class2.html"><span class="doc">dihedral_style class2</span></a>, <a class="reference internal" href="improper_class2.html"><span class="doc">improper_style class2</span></a>, <a class="reference internal" href="pair_class2.html"><span class="doc">pair_style lj/class2</span></a></p> <p>Supporting info: <a class="reference internal" href="bond_class2.html"><span class="doc">bond_style class2</span></a>, <a class="reference internal" href="angle_class2.html"><span class="doc">angle_style class2</span></a>, <a class="reference internal" href="dihedral_class2.html"><span class="doc">dihedral_style class2</span></a>, <a class="reference internal" href="improper_class2.html"><span class="doc">improper_style class2</span></a>, <a class="reference internal" href="pair_class2.html"><span class="doc">pair_style lj/class2</span></a></p>
<hr class="docutils" /> <hr class="docutils" />
</div> </div>
@ -708,9 +708,9 @@ approximation to Stokesian dynamics.</p>
<span class="n">make</span> <span class="n">machine</span> <span class="n">make</span> <span class="n">machine</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">colloid</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span> <pre class="literal-block">
</pre></div> Make.py -p ^colloid -a machine
</div> </pre>
<p>Supporting info: <a class="reference internal" href="fix_wall.html"><span class="doc">fix wall/colloid</span></a>, <a class="reference internal" href="pair_colloid.html"><span class="doc">pair_style colloid</span></a>, <a class="reference internal" href="pair_yukawa_colloid.html"><span class="doc">pair_style yukawa/colloid</span></a>, <a class="reference internal" href="pair_brownian.html"><span class="doc">pair_style brownian</span></a>, <a class="reference internal" href="pair_lubricate.html"><span class="doc">pair_style lubricate</span></a>, <a class="reference internal" href="pair_lubricateU.html"><span class="doc">pair_style lubricateU</span></a>, examples/colloid, examples/srd</p> <p>Supporting info: <a class="reference internal" href="fix_wall.html"><span class="doc">fix wall/colloid</span></a>, <a class="reference internal" href="pair_colloid.html"><span class="doc">pair_style colloid</span></a>, <a class="reference internal" href="pair_yukawa_colloid.html"><span class="doc">pair_style yukawa/colloid</span></a>, <a class="reference internal" href="pair_brownian.html"><span class="doc">pair_style brownian</span></a>, <a class="reference internal" href="pair_lubricate.html"><span class="doc">pair_style lubricate</span></a>, <a class="reference internal" href="pair_lubricateU.html"><span class="doc">pair_style lubricateU</span></a>, examples/colloid, examples/srd</p>
<hr class="docutils" /> <hr class="docutils" />
</div> </div>
@ -737,9 +737,9 @@ zlib info it specifies.</p>
<span class="n">make</span> <span class="n">machine</span> <span class="n">make</span> <span class="n">machine</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">compress</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span> <pre class="literal-block">
</pre></div> Make.py -p ^compress -a machine
</div> </pre>
<p>Supporting info: src/COMPRESS/README, lib/compress/README, <a class="reference internal" href="dump.html"><span class="doc">dump atom/gz</span></a>, <a class="reference internal" href="dump.html"><span class="doc">dump cfg/gz</span></a>, <a class="reference internal" href="dump.html"><span class="doc">dump custom/gz</span></a>, <a class="reference internal" href="dump.html"><span class="doc">dump xyz/gz</span></a></p> <p>Supporting info: src/COMPRESS/README, lib/compress/README, <a class="reference internal" href="dump.html"><span class="doc">dump atom/gz</span></a>, <a class="reference internal" href="dump.html"><span class="doc">dump cfg/gz</span></a>, <a class="reference internal" href="dump.html"><span class="doc">dump custom/gz</span></a>, <a class="reference internal" href="dump.html"><span class="doc">dump xyz/gz</span></a></p>
<hr class="docutils" /> <hr class="docutils" />
</div> </div>
@ -764,9 +764,9 @@ package.</p>
<span class="n">make</span> <span class="n">machine</span> <span class="n">make</span> <span class="n">machine</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">coreshell</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span> <pre class="literal-block">
</pre></div> Make.py -p ^coreshell -a machine
</div> </pre>
<p>Supporting info: <a class="reference internal" href="Section_howto.html#howto-26"><span class="std std-ref">Section howto 6.26</span></a>, <a class="reference internal" href="compute_temp_cs.html"><span class="doc">compute temp/cs</span></a>, <p>Supporting info: <a class="reference internal" href="Section_howto.html#howto-26"><span class="std std-ref">Section howto 6.26</span></a>, <a class="reference internal" href="compute_temp_cs.html"><span class="doc">compute temp/cs</span></a>,
<a class="reference internal" href="pair_cs.html"><span class="doc">pair_style born/coul/long/cs</span></a>, <a class="reference internal" href="pair_cs.html"><span class="doc">pair_style buck/coul/long/cs</span></a>, pair_style <a class="reference internal" href="pair_cs.html"><span class="doc">pair_style born/coul/long/cs</span></a>, <a class="reference internal" href="pair_cs.html"><span class="doc">pair_style buck/coul/long/cs</span></a>, pair_style
lj/cut/coul/long/cs&#8221;_pair_lj.html, examples/coreshell</p> lj/cut/coul/long/cs&#8221;_pair_lj.html, examples/coreshell</p>
@ -789,9 +789,9 @@ dipole models with short-range or long-range interactions.</p>
<span class="n">make</span> <span class="n">machine</span> <span class="n">make</span> <span class="n">machine</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">dipole</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span> <pre class="literal-block">
</pre></div> Make.py -p ^dipole -a machine
</div> </pre>
<p>Supporting info: <a class="reference internal" href="atom_style.html"><span class="doc">atom_style dipole</span></a>, <a class="reference internal" href="pair_dipole.html"><span class="doc">pair_style lj/cut/dipole/cut</span></a>, <a class="reference internal" href="pair_dipole.html"><span class="doc">pair_style lj/cut/dipole/long</span></a>, <a class="reference internal" href="pair_dipole.html"><span class="doc">pair_style lj/long/dipole/long</span></a>, examples/dipole</p> <p>Supporting info: <a class="reference internal" href="atom_style.html"><span class="doc">atom_style dipole</span></a>, <a class="reference internal" href="pair_dipole.html"><span class="doc">pair_style lj/cut/dipole/cut</span></a>, <a class="reference internal" href="pair_dipole.html"><span class="doc">pair_style lj/cut/dipole/long</span></a>, <a class="reference internal" href="pair_dipole.html"><span class="doc">pair_style lj/long/dipole/long</span></a>, examples/dipole</p>
<hr class="docutils" /> <hr class="docutils" />
</div> </div>
@ -841,9 +841,9 @@ one step, with Type &#8220;python src/Make.py -h -gpu&#8221; to see the details.
<span class="n">make</span> <span class="n">machine</span> <span class="n">make</span> <span class="n">machine</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">gpu</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span> <pre class="literal-block">
</pre></div> Make.py -p ^gpu -a machine
</div> </pre>
<p>Supporting info: src/GPU/README, lib/gpu/README, <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section acclerate</span></a>, <a class="reference internal" href="accelerate_gpu.html"><span class="doc">Section accelerate gpu</span></a>, Pair Styles section of <a class="reference internal" href="Section_commands.html#cmd-5"><span class="std std-ref">Section commands 3.5</span></a> for any pair style listed with a (g), <p>Supporting info: src/GPU/README, lib/gpu/README, <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section acclerate</span></a>, <a class="reference internal" href="accelerate_gpu.html"><span class="doc">Section accelerate gpu</span></a>, Pair Styles section of <a class="reference internal" href="Section_commands.html#cmd-5"><span class="std std-ref">Section commands 3.5</span></a> for any pair style listed with a (g),
<a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style</span></a>, <a class="reference internal" href="package.html"><span class="doc">package gpu</span></a>, <a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style</span></a>, <a class="reference internal" href="package.html"><span class="doc">package gpu</span></a>,
examples/accelerate, bench/FERMI, bench/KEPLER</p> examples/accelerate, bench/FERMI, bench/KEPLER</p>
@ -867,9 +867,9 @@ frictional and dissipative potentials.</p>
<span class="n">make</span> <span class="n">machine</span> <span class="n">make</span> <span class="n">machine</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">granular</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span> <pre class="literal-block">
</pre></div> Make.py -p ^granular -a machine
</div> </pre>
<p>Supporting info: <a class="reference internal" href="Section_howto.html#howto-6"><span class="std std-ref">Section howto 6.6</span></a>, <a class="reference internal" href="fix_pour.html"><span class="doc">fix pour</span></a>, <a class="reference internal" href="fix_wall_gran.html"><span class="doc">fix wall/gran</span></a>, <a class="reference internal" href="pair_gran.html"><span class="doc">pair_style gran/hooke</span></a>, <a class="reference internal" href="pair_gran.html"><span class="doc">pair_style gran/hertz/history</span></a>, examples/pour, bench/in.chute</p> <p>Supporting info: <a class="reference internal" href="Section_howto.html#howto-6"><span class="std std-ref">Section howto 6.6</span></a>, <a class="reference internal" href="fix_pour.html"><span class="doc">fix pour</span></a>, <a class="reference internal" href="fix_wall_gran.html"><span class="doc">fix wall/gran</span></a>, <a class="reference internal" href="pair_gran.html"><span class="doc">pair_style gran/hooke</span></a>, <a class="reference internal" href="pair_gran.html"><span class="doc">pair_style gran/hertz/history</span></a>, examples/pour, bench/in.chute</p>
<hr class="docutils" /> <hr class="docutils" />
</div> </div>
@ -896,9 +896,9 @@ process. You should not need to edit this file.</p>
<span class="n">make</span> <span class="n">machine</span> <span class="n">make</span> <span class="n">machine</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">kim</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span> <pre class="literal-block">
</pre></div> Make.py -p ^kim -a machine
</div> </pre>
<p>Supporting info: src/KIM/README, lib/kim/README, <a class="reference internal" href="pair_kim.html"><span class="doc">pair_style kim</span></a>, examples/kim</p> <p>Supporting info: src/KIM/README, lib/kim/README, <a class="reference internal" href="pair_kim.html"><span class="doc">pair_style kim</span></a>, examples/kim</p>
<hr class="docutils" /> <hr class="docutils" />
</div> </div>
@ -928,12 +928,12 @@ choose which hardware to build for. Type &#8220;python src/Make.py -h
system, you will need to read the <a class="reference internal" href="accelerate_kokkos.html"><span class="doc">Section accelerate kokkos</span></a> doc page for details of what system, you will need to read the <a class="reference internal" href="accelerate_kokkos.html"><span class="doc">Section accelerate kokkos</span></a> doc page for details of what
Makefile.machine settings are needed.</p> Makefile.machine settings are needed.</p>
<p>To install via make or Make.py for each of 3 hardware options:</p> <p>To install via make or Make.py for each of 3 hardware options:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">kokkos</span> <pre class="literal-block">
<span class="n">make</span> <span class="n">kokkos_omp</span> <span class="c1"># for CPUs with OpenMP</span> make yes-kokkos
<span class="n">make</span> <span class="n">kokkos_cuda</span> <span class="c1"># for GPUs, check the KOKKOS_ARCH setting in Makefile.kokkos_cuda</span> make kokkos_omp # for CPUs with OpenMP
<span class="n">make</span> <span class="n">kokkos_phi</span> <span class="c1"># for Xeon Phis</span> make kokkos_cuda # for GPUs, check the KOKKOS_ARCH setting in Makefile.kokkos_cuda
</pre></div> make kokkos_phi # for Xeon Phis
</div> </pre>
<p>Make.py -p kokkos -kokkos omp -a machine # for CPUs with OpenMP <p>Make.py -p kokkos -kokkos omp -a machine # for CPUs with OpenMP
Make.py -p kokkos -kokkos cuda arch=35 -a machine # for GPUs of style arch Make.py -p kokkos -kokkos cuda arch=35 -a machine # for GPUs of style arch
Make.py -p kokkos -kokkos phi -a machine # for Xeon Phis</p> Make.py -p kokkos -kokkos phi -a machine # for Xeon Phis</p>
@ -942,9 +942,9 @@ Make.py -p kokkos -kokkos phi -a machine # for Xeon Phis</p>
<span class="n">make</span> <span class="n">machine</span> <span class="n">make</span> <span class="n">machine</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">kokkos</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span> <pre class="literal-block">
</pre></div> Make.py -p ^kokkos -a machine
</div> </pre>
<p>Supporting info: src/KOKKOS/README, lib/kokkos/README, <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section acclerate</span></a>, <a class="reference internal" href="accelerate_kokkos.html"><span class="doc">Section accelerate kokkos</span></a>, Pair Styles section of <a class="reference internal" href="Section_commands.html#cmd-5"><span class="std std-ref">Section commands 3.5</span></a> for any pair style listed <p>Supporting info: src/KOKKOS/README, lib/kokkos/README, <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section acclerate</span></a>, <a class="reference internal" href="accelerate_kokkos.html"><span class="doc">Section accelerate kokkos</span></a>, Pair Styles section of <a class="reference internal" href="Section_commands.html#cmd-5"><span class="std std-ref">Section commands 3.5</span></a> for any pair style listed
with a (k), <a class="reference internal" href="package.html"><span class="doc">package kokkos</span></a>, with a (k), <a class="reference internal" href="package.html"><span class="doc">package kokkos</span></a>,
examples/accelerate, bench/FERMI, bench/KEPLER</p> examples/accelerate, bench/FERMI, bench/KEPLER</p>
@ -977,9 +977,9 @@ see the details.</p>
<span class="n">make</span> <span class="n">machine</span> <span class="n">make</span> <span class="n">machine</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">kspace</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span> <pre class="literal-block">
</pre></div> Make.py -p ^kspace -a machine
</div> </pre>
<p>Supporting info: <a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style</span></a>, <p>Supporting info: <a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style</span></a>,
<a class="reference external" href="PDF/kspace.pdf">doc/PDF/kspace.pdf</a>, <a class="reference internal" href="Section_howto.html#howto-7"><span class="std std-ref">Section howto 6.7</span></a>, <a class="reference internal" href="Section_howto.html#howto-8"><span class="std std-ref">Section howto 6.8</span></a>, <a class="reference internal" href="Section_howto.html#howto-9"><span class="std std-ref">Section howto 6.9</span></a>, <a class="reference internal" href="pair_coul.html"><span class="doc">pair_style coul</span></a>, <a class="reference external" href="PDF/kspace.pdf">doc/PDF/kspace.pdf</a>, <a class="reference internal" href="Section_howto.html#howto-7"><span class="std std-ref">Section howto 6.7</span></a>, <a class="reference internal" href="Section_howto.html#howto-8"><span class="std std-ref">Section howto 6.8</span></a>, <a class="reference internal" href="Section_howto.html#howto-9"><span class="std std-ref">Section howto 6.9</span></a>, <a class="reference internal" href="pair_coul.html"><span class="doc">pair_style coul</span></a>,
other pair style command doc pages which have &#8220;long&#8221; or &#8220;msm&#8221; in their other pair style command doc pages which have &#8220;long&#8221; or &#8220;msm&#8221; in their
@ -1005,9 +1005,9 @@ the full list.</p>
<span class="n">make</span> <span class="n">machine</span> <span class="n">make</span> <span class="n">machine</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">manybody</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span> <pre class="literal-block">
</pre></div> Make.py -p ^manybody -a machine
</div> </pre>
<p>Supporting info:</p> <p>Supporting info:</p>
<p>Examples: Pair Styles section of <a class="reference internal" href="Section_commands.html#cmd-5"><span class="std std-ref">Section commands 3.5</span></a>, examples/comb, examples/eim, <p>Examples: Pair Styles section of <a class="reference internal" href="Section_commands.html#cmd-5"><span class="std std-ref">Section commands 3.5</span></a>, examples/comb, examples/eim,
examples/nb3d, examples/vashishta</p> examples/nb3d, examples/vashishta</p>
@ -1032,9 +1032,9 @@ in conjuction with dynamics.</p>
<span class="n">make</span> <span class="n">machine</span> <span class="n">make</span> <span class="n">machine</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">mc</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span> <pre class="literal-block">
</pre></div> Make.py -p ^mc -a machine
</div> </pre>
<p>Supporting info: <a class="reference internal" href="fix_atom_swap.html"><span class="doc">fix atom/swap</span></a>, <a class="reference internal" href="fix_bond_break.html"><span class="doc">fix bond/break</span></a>, <a class="reference internal" href="fix_bond_create.html"><span class="doc">fix bond/create</span></a>, <a class="reference internal" href="fix_bond_swap.html"><span class="doc">fix bond/swap</span></a>, <p>Supporting info: <a class="reference internal" href="fix_atom_swap.html"><span class="doc">fix atom/swap</span></a>, <a class="reference internal" href="fix_bond_break.html"><span class="doc">fix bond/break</span></a>, <a class="reference internal" href="fix_bond_create.html"><span class="doc">fix bond/create</span></a>, <a class="reference internal" href="fix_bond_swap.html"><span class="doc">fix bond/swap</span></a>,
<a class="reference internal" href="fix_gcmc.html"><span class="doc">fix gcmc</span></a>, <a class="reference internal" href="pair_dsmc.html"><span class="doc">pair_style dsmc</span></a></p> <a class="reference internal" href="fix_gcmc.html"><span class="doc">fix gcmc</span></a>, <a class="reference internal" href="pair_dsmc.html"><span class="doc">pair_style dsmc</span></a></p>
<hr class="docutils" /> <hr class="docutils" />
@ -1079,9 +1079,9 @@ Intel Fortran compiler, rather than the GNU Fortran compiler.</p>
<span class="n">make</span> <span class="n">machine</span> <span class="n">make</span> <span class="n">machine</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">meam</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span> <pre class="literal-block">
</pre></div> Make.py -p ^meam -a machine
</div> </pre>
<p>Supporting info: lib/meam/README, <a class="reference internal" href="pair_meam.html"><span class="doc">pair_style meam</span></a>, <p>Supporting info: lib/meam/README, <a class="reference internal" href="pair_meam.html"><span class="doc">pair_style meam</span></a>,
examples/meam</p> examples/meam</p>
<hr class="docutils" /> <hr class="docutils" />
@ -1104,9 +1104,9 @@ listing, &#8220;ls src/MISC&#8221;, to see the list of commands.</p>
<span class="n">make</span> <span class="n">machine</span> <span class="n">make</span> <span class="n">machine</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">misc</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span> <pre class="literal-block">
</pre></div> Make.py -p ^misc -a machine
</div> </pre>
<p>Supporting info: <a class="reference internal" href="compute_ti.html"><span class="doc">compute ti</span></a>, <a class="reference internal" href="fix_evaporate.html"><span class="doc">fix evaporate</span></a>, <a class="reference internal" href="fix_ttm.html"><span class="doc">fix tmm</span></a>, <a class="reference internal" href="fix_viscosity.html"><span class="doc">fix viscosity</span></a>, examples/misc</p> <p>Supporting info: <a class="reference internal" href="compute_ti.html"><span class="doc">compute ti</span></a>, <a class="reference internal" href="fix_evaporate.html"><span class="doc">fix evaporate</span></a>, <a class="reference internal" href="fix_ttm.html"><span class="doc">fix tmm</span></a>, <a class="reference internal" href="fix_viscosity.html"><span class="doc">fix viscosity</span></a>, examples/misc</p>
<hr class="docutils" /> <hr class="docutils" />
</div> </div>
@ -1129,9 +1129,9 @@ covalent bonds. The pair styles include terms for the Dreiding
<span class="n">make</span> <span class="n">machine</span> <span class="n">make</span> <span class="n">machine</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">molecule</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span> <pre class="literal-block">
</pre></div> Make.py -p ^molecule -a machine
</div> </pre>
<p>Supporting info:<a class="reference internal" href="atom_style.html"><span class="doc">atom_style</span></a>, <p>Supporting info:<a class="reference internal" href="atom_style.html"><span class="doc">atom_style</span></a>,
<a class="reference internal" href="bond_style.html"><span class="doc">bond_style</span></a>, <a class="reference internal" href="angle_style.html"><span class="doc">angle_style</span></a>, <a class="reference internal" href="bond_style.html"><span class="doc">bond_style</span></a>, <a class="reference internal" href="angle_style.html"><span class="doc">angle_style</span></a>,
<a class="reference internal" href="dihedral_style.html"><span class="doc">dihedral_style</span></a>, <a class="reference internal" href="dihedral_style.html"><span class="doc">dihedral_style</span></a>,
@ -1159,9 +1159,9 @@ are also written and read in parallel.</p>
<span class="n">make</span> <span class="n">machine</span> <span class="n">make</span> <span class="n">machine</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">mpiio</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span> <pre class="literal-block">
</pre></div> Make.py -p ^mpiio -a machine
</div> </pre>
<p>Supporting info: <a class="reference internal" href="dump.html"><span class="doc">dump</span></a>, <a class="reference internal" href="restart.html"><span class="doc">restart</span></a>, <p>Supporting info: <a class="reference internal" href="dump.html"><span class="doc">dump</span></a>, <a class="reference internal" href="restart.html"><span class="doc">restart</span></a>,
<a class="reference internal" href="write_restart.html"><span class="doc">write_restart</span></a>, <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a></p> <a class="reference internal" href="write_restart.html"><span class="doc">write_restart</span></a>, <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a></p>
<hr class="docutils" /> <hr class="docutils" />
@ -1192,9 +1192,9 @@ creates and uses.</p>
<span class="n">make</span> <span class="n">machine</span> <span class="n">make</span> <span class="n">machine</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">opt</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span> <pre class="literal-block">
</pre></div> Make.py -p ^opt -a machine
</div> </pre>
<p>Supporting info: <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section acclerate</span></a>, <a class="reference internal" href="accelerate_opt.html"><span class="doc">Section accelerate opt</span></a>, Pair Styles section of <a class="reference internal" href="Section_commands.html#cmd-5"><span class="std std-ref">Section commands 3.5</span></a> for any pair style listed <p>Supporting info: <a class="reference internal" href="Section_accelerate.html"><span class="doc">Section acclerate</span></a>, <a class="reference internal" href="accelerate_opt.html"><span class="doc">Section accelerate opt</span></a>, Pair Styles section of <a class="reference internal" href="Section_commands.html#cmd-5"><span class="std std-ref">Section commands 3.5</span></a> for any pair style listed
with an (o), examples/accelerate, bench/KEPLER</p> with an (o), examples/accelerate, bench/KEPLER</p>
<hr class="docutils" /> <hr class="docutils" />
@ -1218,9 +1218,9 @@ styles which implement different materials models.</p>
<span class="n">make</span> <span class="n">machine</span> <span class="n">make</span> <span class="n">machine</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">peri</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span> <pre class="literal-block">
</pre></div> Make.py -p ^peri -a machine
</div> </pre>
<p>Supporting info: <p>Supporting info:
<a class="reference external" href="PDF/PDLammps_overview.pdf">doc/PDF/PDLammps_overview.pdf</a>, <a class="reference external" href="PDF/PDLammps_overview.pdf">doc/PDF/PDLammps_overview.pdf</a>,
<a class="reference external" href="PDF/PDLammps_EPS.pdf">doc/PDF/PDLammps_EPS.pdf</a>, <a class="reference external" href="PDF/PDLammps_EPS.pdf">doc/PDF/PDLammps_EPS.pdf</a>,
@ -1261,9 +1261,9 @@ one step. Type &#8220;python src/Make.py -h -poems&#8221; to see the details.</
<span class="n">make</span> <span class="n">machine</span> <span class="n">make</span> <span class="n">machine</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">meam</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span> <pre class="literal-block">
</pre></div> Make.py -p ^meam -a machine
</div> </pre>
<p>Supporting info: src/POEMS/README, lib/poems/README, <p>Supporting info: src/POEMS/README, lib/poems/README,
<a class="reference internal" href="fix_poems.html"><span class="doc">fix poems</span></a>, examples/rigid</p> <a class="reference internal" href="fix_poems.html"><span class="doc">fix poems</span></a>, examples/rigid</p>
<hr class="docutils" /> <hr class="docutils" />
@ -1296,9 +1296,9 @@ in one step. Type &#8220;python src/Make.py -h -python&#8221; to see the detail
<span class="n">make</span> <span class="n">machine</span> <span class="n">make</span> <span class="n">machine</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">python</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span> <pre class="literal-block">
</pre></div> Make.py -p ^python -a machine
</div> </pre>
<p>Supporting info: examples/python</p> <p>Supporting info: examples/python</p>
<hr class="docutils" /> <hr class="docutils" />
</div> </div>
@ -1320,9 +1320,9 @@ that use QEq as part of their formulation.</p>
<span class="n">make</span> <span class="n">machine</span> <span class="n">make</span> <span class="n">machine</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">qeq</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span> <pre class="literal-block">
</pre></div> Make.py -p ^qeq -a machine
</div> </pre>
<p>Supporting info: <a class="reference internal" href="fix_qeq.html"><span class="doc">fix qeq/*</span></a>, examples/qeq</p> <p>Supporting info: <a class="reference internal" href="fix_qeq.html"><span class="doc">fix qeq/*</span></a>, examples/qeq</p>
<hr class="docutils" /> <hr class="docutils" />
</div> </div>
@ -1362,9 +1362,9 @@ one step. Type &#8220;python src/Make.py -h -reax&#8221; to see the details.</p
<span class="n">make</span> <span class="n">machine</span> <span class="n">make</span> <span class="n">machine</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">reax</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span> <pre class="literal-block">
</pre></div> Make.py -p ^reax -a machine
</div> </pre>
<p>Supporting info: lib/reax/README, <a class="reference internal" href="pair_reax.html"><span class="doc">pair_style reax</span></a>, <p>Supporting info: lib/reax/README, <a class="reference internal" href="pair_reax.html"><span class="doc">pair_style reax</span></a>,
<a class="reference internal" href="fix_reax_bonds.html"><span class="doc">fix reax/bonds</span></a>, examples/reax</p> <a class="reference internal" href="fix_reax_bonds.html"><span class="doc">fix reax/bonds</span></a>, examples/reax</p>
<hr class="docutils" /> <hr class="docutils" />
@ -1394,9 +1394,9 @@ field calcalation on another set.</p>
<span class="n">make</span> <span class="n">machine</span> <span class="n">make</span> <span class="n">machine</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">replica</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span> <pre class="literal-block">
</pre></div> Make.py -p ^replica -a machine
</div> </pre>
<p>Supporting info: <a class="reference internal" href="Section_howto.html#howto-5"><span class="std std-ref">Section howto 6.5</span></a>, <p>Supporting info: <a class="reference internal" href="Section_howto.html#howto-5"><span class="std std-ref">Section howto 6.5</span></a>,
<a class="reference internal" href="neb.html"><span class="doc">neb</span></a>, <a class="reference internal" href="prd.html"><span class="doc">prd</span></a>, <a class="reference internal" href="tad.html"><span class="doc">tad</span></a>, <a class="reference internal" href="temper.html"><span class="doc">temper</span></a>, <a class="reference internal" href="neb.html"><span class="doc">neb</span></a>, <a class="reference internal" href="prd.html"><span class="doc">prd</span></a>, <a class="reference internal" href="tad.html"><span class="doc">tad</span></a>, <a class="reference internal" href="temper.html"><span class="doc">temper</span></a>,
<a class="reference internal" href="run_style.html"><span class="doc">run_style verlet/split</span></a>, examples/neb, examples/prd, <a class="reference internal" href="run_style.html"><span class="doc">run_style verlet/split</span></a>, examples/neb, examples/prd,
@ -1422,9 +1422,9 @@ few large bodies or many small bodies.</p>
<span class="n">make</span> <span class="n">machine</span> <span class="n">make</span> <span class="n">machine</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">rigid</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span> <pre class="literal-block">
</pre></div> Make.py -p ^rigid -a machine
</div> </pre>
<p>Supporting info: <a class="reference internal" href="compute_erotate_rigid.html"><span class="doc">compute erotate/rigid</span></a>, <p>Supporting info: <a class="reference internal" href="compute_erotate_rigid.html"><span class="doc">compute erotate/rigid</span></a>,
<a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a>, <a class="reference internal" href="fix_shake.html"><span class="doc">fix rattle</span></a>, <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid/*</span></a>, examples/ASPHERE, examples/rigid</p> <a class="reference internal" href="fix_shake.html"><span class="doc">fix shake</span></a>, <a class="reference internal" href="fix_shake.html"><span class="doc">fix rattle</span></a>, <a class="reference internal" href="fix_rigid.html"><span class="doc">fix rigid/*</span></a>, examples/ASPHERE, examples/rigid</p>
<hr class="docutils" /> <hr class="docutils" />
@ -1446,9 +1446,9 @@ simulations where a shock-wave passes through a material.</p>
<span class="n">make</span> <span class="n">machine</span> <span class="n">make</span> <span class="n">machine</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">shock</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span> <pre class="literal-block">
</pre></div> Make.py -p ^shock -a machine
</div> </pre>
<p>Supporting info: <a class="reference internal" href="fix_append_atoms.html"><span class="doc">fix append/atoms</span></a>, <a class="reference internal" href="fix_msst.html"><span class="doc">fix msst</span></a>, <a class="reference internal" href="fix_nphug.html"><span class="doc">fix nphug</span></a>, <a class="reference internal" href="fix_wall_piston.html"><span class="doc">fix wall/piston</span></a>, examples/hugoniostat, examples/msst</p> <p>Supporting info: <a class="reference internal" href="fix_append_atoms.html"><span class="doc">fix append/atoms</span></a>, <a class="reference internal" href="fix_msst.html"><span class="doc">fix msst</span></a>, <a class="reference internal" href="fix_nphug.html"><span class="doc">fix nphug</span></a>, <a class="reference internal" href="fix_wall_piston.html"><span class="doc">fix wall/piston</span></a>, examples/hugoniostat, examples/msst</p>
<hr class="docutils" /> <hr class="docutils" />
</div> </div>
@ -1471,9 +1471,9 @@ properties of the potential are also included.</p>
<span class="n">make</span> <span class="n">machine</span> <span class="n">make</span> <span class="n">machine</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">snap</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span> <pre class="literal-block">
</pre></div> Make.py -p ^snap -a machine
</div> </pre>
<p>Supporting info: <a class="reference internal" href="pair_snap.html"><span class="doc">pair snap</span></a>, <a class="reference internal" href="compute_sna_atom.html"><span class="doc">compute sna/atom</span></a>, <a class="reference internal" href="compute_sna_atom.html"><span class="doc">compute snad/atom</span></a>, <p>Supporting info: <a class="reference internal" href="pair_snap.html"><span class="doc">pair snap</span></a>, <a class="reference internal" href="compute_sna_atom.html"><span class="doc">compute sna/atom</span></a>, <a class="reference internal" href="compute_sna_atom.html"><span class="doc">compute snad/atom</span></a>,
<a class="reference internal" href="compute_sna_atom.html"><span class="doc">compute snav/atom</span></a>, examples/snap</p> <a class="reference internal" href="compute_sna_atom.html"><span class="doc">compute snav/atom</span></a>, examples/snap</p>
<hr class="docutils" /> <hr class="docutils" />
@ -1496,9 +1496,9 @@ colloidal-scale particles.</p>
<span class="n">make</span> <span class="n">machine</span> <span class="n">make</span> <span class="n">machine</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">srd</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span> <pre class="literal-block">
</pre></div> Make.py -p ^srd -a machine
</div> </pre>
<p>Supporting info: <a class="reference internal" href="fix_srd.html"><span class="doc">fix srd</span></a>, <a class="reference internal" href="fix_wall_srd.html"><span class="doc">fix wall/srd</span></a>, examples/srd, examples/ASPHERE</p> <p>Supporting info: <a class="reference internal" href="fix_srd.html"><span class="doc">fix srd</span></a>, <a class="reference internal" href="fix_wall_srd.html"><span class="doc">fix wall/srd</span></a>, examples/srd, examples/ASPHERE</p>
<hr class="docutils" /> <hr class="docutils" />
</div> </div>
@ -1541,9 +1541,9 @@ src/Make.py -h -voronoi&#8221; to see the details.</p>
<span class="n">make</span> <span class="n">machine</span> <span class="n">make</span> <span class="n">machine</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">voronoi</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span> <pre class="literal-block">
</pre></div> Make.py -p ^voronoi -a machine
</div> </pre>
<p>Supporting info: src/VORONOI/README, lib/voronoi/README, <a class="reference internal" href="compute_voronoi_atom.html"><span class="doc">compute voronoi/atom</span></a>, examples/voronoi</p> <p>Supporting info: src/VORONOI/README, lib/voronoi/README, <a class="reference internal" href="compute_voronoi_atom.html"><span class="doc">compute voronoi/atom</span></a>, examples/voronoi</p>
<hr class="docutils" /> <hr class="docutils" />
</div> </div>
@ -1860,7 +1860,7 @@ src/Make.py -h -voronoi&#8221; to see the details.</p>
<tr class="row-even"><td><a class="reference internal" href="#user-smd"><span class="std std-ref">USER-SMD</span></a></td> <tr class="row-even"><td><a class="reference internal" href="#user-smd"><span class="std std-ref">USER-SMD</span></a></td>
<td>smoothed Mach dynamics</td> <td>smoothed Mach dynamics</td>
<td>Georg Ganzenmuller (EMI)</td> <td>Georg Ganzenmuller (EMI)</td>
<td><a class="reference external" href="PDF/SMD_LAMMPS_userguide.pdf">userguide.pdf</a></td> <td><a class="reference external" href="PDF/SMD_LAMMPS_userguide.pdf">SMD User Guide</a></td>
<td>USER/smd</td> <td>USER/smd</td>
<td><ul class="first last simple"> <td><ul class="first last simple">
<li></li> <li></li>
@ -1888,7 +1888,7 @@ src/Make.py -h -voronoi&#8221; to see the details.</p>
<tr class="row-even"><td><a class="reference internal" href="#user-sph"><span class="std std-ref">USER-SPH</span></a></td> <tr class="row-even"><td><a class="reference internal" href="#user-sph"><span class="std std-ref">USER-SPH</span></a></td>
<td>smoothed particle hydrodynamics</td> <td>smoothed particle hydrodynamics</td>
<td>Georg Ganzenmuller (EMI)</td> <td>Georg Ganzenmuller (EMI)</td>
<td><a class="reference external" href="PDF/SPH_LAMMPS_userguide.pdf">userguide.pdf</a></td> <td><a class="reference external" href="PDF/SPH_LAMMPS_userguide.pdf">SPH User Guide</a></td>
<td>USER/sph</td> <td>USER/sph</td>
<td><a class="reference external" href="http://lammps.sandia.gov/movies.html#sph">sph</a></td> <td><a class="reference external" href="http://lammps.sandia.gov/movies.html#sph">sph</a></td>
<td><ul class="first last simple"> <td><ul class="first last simple">
@ -1986,9 +1986,9 @@ more details.</p>
<span class="n">make</span> <span class="n">machine</span> <span class="n">make</span> <span class="n">machine</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="o">^</span><span class="n">atc</span> <span class="o">-</span><span class="n">a</span> <span class="n">machine</span> <pre class="literal-block">
</pre></div> Make.py -p ^atc -a machine
</div> </pre>
<p>Supporting <a class="reference external" href="info:src/USER-ATC/README">info:src/USER-ATC/README</a>, <a class="reference internal" href="fix_atc.html"><span class="doc">fix atc</span></a>, <p>Supporting <a class="reference external" href="info:src/USER-ATC/README">info:src/USER-ATC/README</a>, <a class="reference internal" href="fix_atc.html"><span class="doc">fix atc</span></a>,
examples/USER/atc</p> examples/USER/atc</p>
<p>Authors: Reese Jones (rjones at sandia.gov), Jeremy Templeton (jatempl <p>Authors: Reese Jones (rjones at sandia.gov), Jeremy Templeton (jatempl
@ -2064,10 +2064,9 @@ equations of motion are integrated efficiently through the Shardlow
splitting algorithm. See src/USER-DPD/README for more details.</p> splitting algorithm. See src/USER-DPD/README for more details.</p>
<p>Supporting info: /src/USER-DPD/README, <a class="reference internal" href="compute_dpd.html"><span class="doc">compute dpd</span></a> <p>Supporting info: /src/USER-DPD/README, <a class="reference internal" href="compute_dpd.html"><span class="doc">compute dpd</span></a>
<a class="reference internal" href="compute_dpd_atom.html"><span class="doc">compute dpd/atom</span></a> <a class="reference internal" href="compute_dpd_atom.html"><span class="doc">compute dpd/atom</span></a>
<a class="reference internal" href="fix_eos_table.html"><span class="doc">fix eos/cv</span></a> <a class="reference internal" href="fix_eos_table.html"><span class="doc">fix eos/table</span></a></p> <a class="reference internal" href="fix_eos_table.html"><span class="doc">fix eos/cv</span></a> <a class="reference internal" href="fix_eos_table.html"><span class="doc">fix eos/table</span></a>
<blockquote> <a class="reference internal" href="fix_eos_table_rx.html"><span class="doc">fix eos/table/rx</span></a> <a class="reference internal" href="fix_shardlow.html"><span class="doc">fix shardlow</span></a>
<div><a class="reference internal" href="fix_eos_table_rx.html"><span class="doc">fix eos/table/rx</span></a> <a class="reference internal" href="fix_shardlow.html"><span class="doc">fix shardlow</span></a></div></blockquote> <a class="reference internal" href="fix_rx.html"><span class="doc">fix rx</span></a> <a class="reference internal" href="pair_table_rx.html"><span class="doc">pair table/rx</span></a>
<p><a class="reference internal" href="fix_rx.html"><span class="doc">fix rx</span></a> <a class="reference internal" href="pair_table_rx.html"><span class="doc">pair table/rx</span></a>
<a class="reference internal" href="pair_dpd_fdt.html"><span class="doc">pair dpd/fdt</span></a> <a class="reference internal" href="pair_dpd_fdt.html"><span class="doc">pair dpd/fdt/energy</span></a> <a class="reference internal" href="pair_dpd_fdt.html"><span class="doc">pair dpd/fdt</span></a> <a class="reference internal" href="pair_dpd_fdt.html"><span class="doc">pair dpd/fdt/energy</span></a>
<a class="reference internal" href="pair_exp6_rx.html"><span class="doc">pair exp6/rx</span></a> <a class="reference internal" href="pair_multi_lucy.html"><span class="doc">pair multi/lucy</span></a> <a class="reference internal" href="pair_exp6_rx.html"><span class="doc">pair exp6/rx</span></a> <a class="reference internal" href="pair_multi_lucy.html"><span class="doc">pair multi/lucy</span></a>
<a class="reference internal" href="pair_multi_lucy_rx.html"><span class="doc">pair multi/lucy/rx</span></a>, examples/USER/dpd</p> <a class="reference internal" href="pair_multi_lucy_rx.html"><span class="doc">pair multi/lucy/rx</span></a>, examples/USER/dpd</p>
@ -2213,7 +2212,7 @@ Contact them directly if you have any questions.</p>
<p>Supporting info:</p> <p>Supporting info:</p>
<p>The files in this package are a potpourri of (mostly) unrelated <p>The files in this package are a potpourri of (mostly) unrelated
features contributed to LAMMPS by users. Each feature is a single features contributed to LAMMPS by users. Each feature is a single
pair of files (<a href="#id2"><span class="problematic" id="id3">*</span></a>.cpp and <a href="#id4"><span class="problematic" id="id5">*</span></a>.h).</p> pair of files (*.cpp and *.h).</p>
<p>More information about each feature can be found by reading its doc <p>More information about each feature can be found by reading its doc
page in the LAMMPS doc directory. The doc page which lists all LAMMPS page in the LAMMPS doc directory. The doc page which lists all LAMMPS
input script commands is as follows:</p> input script commands is as follows:</p>
@ -2382,18 +2381,18 @@ questions.</p>
<p>Supporting info:</p> <p>Supporting info:</p>
<p>This package implements smoothed Mach dynamics (SMD) in <p>This package implements smoothed Mach dynamics (SMD) in
LAMMPS. Currently, the package has the following features:</p> LAMMPS. Currently, the package has the following features:</p>
<ul class="simple"> <p>* Does liquids via traditional Smooth Particle Hydrodynamics (SPH)</p>
<li>Does liquids via traditional Smooth Particle Hydrodynamics (SPH)</li> <dl class="docutils">
<li>Also solves solids mechanics problems via a state of the art <dt>* Also solves solids mechanics problems via a state of the art</dt>
stabilized meshless method with hourglass control.</li> <dd>stabilized meshless method with hourglass control.</dd>
<li>Can specify hydrostatic interactions independently from material <dt>* Can specify hydrostatic interactions independently from material</dt>
strength models, i.e. pressure and deviatoric stresses are separated.</li> <dd>strength models, i.e. pressure and deviatoric stresses are separated.</dd>
<li>Many material models available (Johnson-Cook, plasticity with <dt>* Many material models available (Johnson-Cook, plasticity with</dt>
hardening, Mie-Grueneisen, Polynomial EOS). Easy to add new <dd>hardening, Mie-Grueneisen, Polynomial EOS). Easy to add new
material models.</li> material models.</dd>
<li>Rigid boundary conditions (walls) can be loaded as surface geometries <dt>* Rigid boundary conditions (walls) can be loaded as surface geometries</dt>
from <a href="#id8"><span class="problematic" id="id9">*</span></a>.STL files.</li> <dd>from *.STL files.</dd>
</ul> </dl>
<p>See the file doc/PDF/SMD_LAMMPS_userguide.pdf to get started.</p> <p>See the file doc/PDF/SMD_LAMMPS_userguide.pdf to get started.</p>
<p>There are example scripts for using this package in examples/USER/smd.</p> <p>There are example scripts for using this package in examples/USER/smd.</p>
<p>The person who created this package is Georg Ganzenmuller at the <p>The person who created this package is Georg Ganzenmuller at the
@ -2424,16 +2423,18 @@ them directly if you have any questions.</p>
<p>Supporting info:</p> <p>Supporting info:</p>
<p>This package implements smoothed particle hydrodynamics (SPH) in <p>This package implements smoothed particle hydrodynamics (SPH) in
LAMMPS. Currently, the package has the following features:</p> LAMMPS. Currently, the package has the following features:</p>
<ul class="simple"> <dl class="docutils">
<li>Tait, ideal gas, Lennard-Jones equation of states, full support for <dt>* Tait, ideal gas, Lennard-Jones equation of states, full support for</dt>
complete (i.e. internal-energy dependent) equations of state</li> <dd>complete (i.e. internal-energy dependent) equations of state</dd>
<li>Plain or Monaghans XSPH integration of the equations of motion</li> </dl>
<li>Density continuity or density summation to propagate the density field</li> <p>* Plain or Monaghans XSPH integration of the equations of motion</p>
<li>Commands to set internal energy and density of particles from the <p>* Density continuity or density summation to propagate the density field</p>
input script</li> <dl class="docutils">
<li>Output commands to access internal energy and density for dumping and <dt>* Commands to set internal energy and density of particles from the</dt>
thermo output</li> <dd>input script</dd>
</ul> <dt>* Output commands to access internal energy and density for dumping and</dt>
<dd>thermo output</dd>
</dl>
<p>See the file doc/PDF/SPH_LAMMPS_userguide.pdf to get started.</p> <p>See the file doc/PDF/SPH_LAMMPS_userguide.pdf to get started.</p>
<p>There are example scripts for using this package in examples/USER/sph.</p> <p>There are example scripts for using this package in examples/USER/sph.</p>
<p>The person who created this package is Georg Ganzenmuller at the <p>The person who created this package is Georg Ganzenmuller at the

250
doc/html/Section_python.html
View File

@ -343,10 +343,10 @@ described above.</p>
<p>If you set the paths to these files as environment variables, you only <p>If you set the paths to these files as environment variables, you only
have to do it once. For the csh or tcsh shells, add something like have to do it once. For the csh or tcsh shells, add something like
this to your ~/.cshrc file, one line for each of the two files:</p> this to your ~/.cshrc file, one line for each of the two files:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span>setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/python <pre class="literal-block">
setenv PYTHONPATH ${PYTHONPATH}:/home/sjplimp/lammps/python
setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src
</pre></div> </pre>
</div>
<p>If you use the python/install.py script, you need to invoke it every <p>If you use the python/install.py script, you need to invoke it every
time you rebuild LAMMPS (as a shared library) or make changes to the time you rebuild LAMMPS (as a shared library) or make changes to the
python/lammps.py file.</p> python/lammps.py file.</p>
@ -393,39 +393,21 @@ environment variable as described above.</p>
your Python with an interface to MPI. This also allows you to your Python with an interface to MPI. This also allows you to
make MPI calls directly from Python in your script, if you desire.</p> make MPI calls directly from Python in your script, if you desire.</p>
<p>There are several Python packages available that purport to wrap MPI <p>There are several Python packages available that purport to wrap MPI
as a library and allow MPI functions to be called from Python.</p> as a library and allow MPI functions to be called from Python. However,
<p>These include</p> development on most of them seems to be halted except on:</p>
<ul class="simple"> <ul class="simple">
<li><a class="reference external" href="http://pympi.sourceforge.net/">pyMPI</a></li> <li><a class="reference external" href="https://bitbucket.org/mpi4py/mpi4py">mpi4py</a></li>
<li><a class="reference external" href="http://code.google.com/p/maroonmpi/">maroonmpi</a></li> <li><a class="reference external" href="https://github.com/daleroberts/pypar">PyPar</a></li>
<li><a class="reference external" href="http://code.google.com/p/mpi4py/">mpi4py</a></li>
<li><a class="reference external" href="http://nbcr.sdsc.edu/forum/viewtopic.php?t=89&amp;sid=c997fefc3933bd66204875b436940f16">myMPI</a></li>
<li><a class="reference external" href="http://code.google.com/p/pypar">Pypar</a></li>
</ul> </ul>
<p>All of these except pyMPI work by wrapping the MPI library and <p>Both packages, PyPar and mpi4py have been successfully tested with
exposing (some portion of) its interface to your Python script. This LAMMPS. PyPar is simpler and easy to set up and use, but supports
means Python cannot be used interactively in parallel, since they do
not address the issue of interactive input to multiple instances of
Python running on different processors. The one exception is pyMPI,
which alters the Python interpreter to address this issue, and (I
believe) creates a new alternate executable (in place of &#8220;python&#8221;
itself) as a result.</p>
<p>In principle any of these Python/MPI packages should work to invoke
LAMMPS in parallel and to make MPI calls themselves from a Python
script which is itself running in parallel. However, when I
downloaded and looked at a few of them, their documentation was
incomplete and I had trouble with their installation. It&#8217;s not clear
if some of the packages are still being actively developed and
supported.</p>
<p>The packages Pypar and mpi4py have both been successfully tested with
LAMMPS. Pypar is simpler and easy to set up and use, but supports
only a subset of MPI. Mpi4py is more MPI-feature complete, but also a only a subset of MPI. Mpi4py is more MPI-feature complete, but also a
bit more complex to use. As of version 2.0.0, mpi4py is the only bit more complex to use. As of version 2.0.0, mpi4py is the only
python MPI wrapper that allows passing a custom MPI communicator to python MPI wrapper that allows passing a custom MPI communicator to
the LAMMPS constructor, which means one can easily run one or more the LAMMPS constructor, which means one can easily run one or more
LAMMPS instances on subsets of the total MPI ranks.</p> LAMMPS instances on subsets of the total MPI ranks.</p>
<hr class="docutils" /> <hr class="docutils" />
<p>Pypar requires the ubiquitous <a class="reference external" href="http://numpy.scipy.org">Numpy package</a> <p>PyPar requires the ubiquitous <a class="reference external" href="http://numpy.scipy.org">Numpy package</a>
be installed in your Python. After launching Python, type</p> be installed in your Python. After launching Python, type</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">numpy</span> <div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">numpy</span>
</pre></div> </pre></div>
@ -439,15 +421,15 @@ top-level directory, type</p>
</div> </div>
<p>The &#8220;sudo&#8221; is only needed if required to copy Numpy files into your <p>The &#8220;sudo&#8221; is only needed if required to copy Numpy files into your
Python distribution&#8217;s site-packages directory.</p> Python distribution&#8217;s site-packages directory.</p>
<p>To install Pypar (version pypar-2.1.4_94 as of Aug 2012), unpack it <p>To install PyPar (version pypar-2.1.4_94 as of Aug 2012), unpack it
and from its &#8220;source&#8221; directory, type</p> and from its &#8220;source&#8221; directory, type</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">build</span> <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">build</span>
<span class="n">sudo</span> <span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">install</span> <span class="n">sudo</span> <span class="n">python</span> <span class="n">setup</span><span class="o">.</span><span class="n">py</span> <span class="n">install</span>
</pre></div> </pre></div>
</div> </div>
<p>Again, the &#8220;sudo&#8221; is only needed if required to copy Pypar files into <p>Again, the &#8220;sudo&#8221; is only needed if required to copy PyPar files into
your Python distribution&#8217;s site-packages directory.</p> your Python distribution&#8217;s site-packages directory.</p>
<p>If you have successully installed Pypar, you should be able to run <p>If you have successully installed PyPar, you should be able to run
Python and type</p> Python and type</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">pypar</span> <div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">pypar</span>
</pre></div> </pre></div>
@ -465,17 +447,17 @@ on a simple test script</p>
<p>and see one line of output for each processor you run on.</p> <p>and see one line of output for each processor you run on.</p>
<div class="admonition note"> <div class="admonition note">
<p class="first admonition-title">Note</p> <p class="first admonition-title">Note</p>
<p class="last">To use Pypar and LAMMPS in parallel from Python, you must insure <p class="last">To use PyPar and LAMMPS in parallel from Python, you must insure
both are using the same version of MPI. If you only have one MPI both are using the same version of MPI. If you only have one MPI
installed on your system, this is not an issue, but it can be if you installed on your system, this is not an issue, but it can be if you
have multiple MPIs. Your LAMMPS build is explicit about which MPI it have multiple MPIs. Your LAMMPS build is explicit about which MPI it
is using, since you specify the details in your lo-level is using, since you specify the details in your lo-level
src/MAKE/Makefile.foo file. Pypar uses the &#8220;mpicc&#8221; command to find src/MAKE/Makefile.foo file. PyPar uses the &#8220;mpicc&#8221; command to find
information about the MPI it uses to build against. And it tries to information about the MPI it uses to build against. And it tries to
load &#8220;libmpi.so&#8221; from the LD_LIBRARY_PATH. This may or may not find load &#8220;libmpi.so&#8221; from the LD_LIBRARY_PATH. This may or may not find
the MPI library that LAMMPS is using. If you have problems running the MPI library that LAMMPS is using. If you have problems running
both Pypar and LAMMPS together, this is an issue you may need to both PyPar and LAMMPS together, this is an issue you may need to
address, e.g. by moving other MPI installations so that Pypar finds address, e.g. by moving other MPI installations so that PyPar finds
the right one.</p> the right one.</p>
</div> </div>
<hr class="docutils" /> <hr class="docutils" />
@ -502,11 +484,11 @@ on a simple test script</p>
</pre></div> </pre></div>
</div> </div>
<p>where test.py contains the lines</p> <p>where test.py contains the lines</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">mpi4py</span> <span class="k">import</span> <span class="n">MPI</span> <pre class="literal-block">
<span class="n">comm</span> <span class="o">=</span> <span class="n">MPI</span><span class="o">.</span><span class="n">COMM_WORLD</span> from mpi4py import MPI
<span class="nb">print</span> <span class="s2">&quot;Proc </span><span class="si">%d</span><span class="s2"> out of </span><span class="si">%d</span><span class="s2"> procs&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">comm</span><span class="o">.</span><span class="n">Get_rank</span><span class="p">(),</span><span class="n">comm</span><span class="o">.</span><span class="n">Get_size</span><span class="p">())</span> comm = MPI.COMM_WORLD
</pre></div> print &quot;Proc %d out of %d procs&quot; % (comm.Get_rank(),comm.Get_size())
</div> </pre>
<p>and see one line of output for each processor you run on.</p> <p>and see one line of output for each processor you run on.</p>
<div class="admonition note"> <div class="admonition note">
<p class="first admonition-title">Note</p> <p class="first admonition-title">Note</p>
@ -568,15 +550,15 @@ interactively from the bench directory:</p>
<p>Either way, you should see the results of running the in.lj benchmark <p>Either way, you should see the results of running the in.lj benchmark
on a single processor appear on the screen, the same as if you had on a single processor appear on the screen, the same as if you had
typed something like:</p> typed something like:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_g</span><span class="o">++</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <pre class="literal-block">
</pre></div> lmp_g++ -in in.lj
</div> </pre>
</div> </div>
<div class="section" id="test-lammps-and-python-in-parallel"> <div class="section" id="test-lammps-and-python-in-parallel">
<h3>11.6.2. <strong>Test LAMMPS and Python in parallel:</strong></h3> <h3>11.6.2. <strong>Test LAMMPS and Python in parallel:</strong></h3>
<p>To run LAMMPS in parallel, assuming you have installed the <p>To run LAMMPS in parallel, assuming you have installed the
<a class="reference external" href="Pypar">Pypar</a> package as discussed above, create a test.py file <a class="reference external" href="https://github.com/daleroberts/pypar">PyPar</a> package as discussed
containing these lines:</p> above, create a test.py file containing these lines:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">pypar</span> <div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">pypar</span>
<span class="kn">from</span> <span class="nn">lammps</span> <span class="k">import</span> <span class="n">lammps</span> <span class="kn">from</span> <span class="nn">lammps</span> <span class="k">import</span> <span class="n">lammps</span>
<span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">()</span> <span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">()</span>
@ -586,36 +568,36 @@ containing these lines:</p>
</pre></div> </pre></div>
</div> </div>
<p>To run LAMMPS in parallel, assuming you have installed the <p>To run LAMMPS in parallel, assuming you have installed the
<a class="reference external" href="mpi4py">mpi4py</a> package as discussed above, create a test.py file <a class="reference external" href="https://bitbucket.org/mpi4py/mpi4py">mpi4py</a> package as discussed
containing these lines:</p> above, create a test.py file containing these lines:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">mpi4py</span> <span class="k">import</span> <span class="n">MPI</span> <pre class="literal-block">
<span class="kn">from</span> <span class="nn">lammps</span> <span class="k">import</span> <span class="n">lammps</span> from mpi4py import MPI
<span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">()</span> from lammps import lammps
<span class="n">lmp</span><span class="o">.</span><span class="n">file</span><span class="p">(</span><span class="s2">&quot;in.lj&quot;</span><span class="p">)</span> lmp = lammps()
<span class="n">me</span> <span class="o">=</span> <span class="n">MPI</span><span class="o">.</span><span class="n">COMM_WORLD</span><span class="o">.</span><span class="n">Get_rank</span><span class="p">()</span> lmp.file(&quot;in.lj&quot;)
<span class="n">nprocs</span> <span class="o">=</span> <span class="n">MPI</span><span class="o">.</span><span class="n">COMM_WORLD</span><span class="o">.</span><span class="n">Get_size</span><span class="p">()</span> me = MPI.COMM_WORLD.Get_rank()
<span class="nb">print</span> <span class="s2">&quot;Proc </span><span class="si">%d</span><span class="s2"> out of </span><span class="si">%d</span><span class="s2"> procs has&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">me</span><span class="p">,</span><span class="n">nprocs</span><span class="p">),</span><span class="n">lmp</span> nprocs = MPI.COMM_WORLD.Get_size()
<span class="n">MPI</span><span class="o">.</span><span class="n">Finalize</span><span class="p">()</span> print &quot;Proc %d out of %d procs has&quot; % (me,nprocs),lmp
</pre></div> MPI.Finalize()
</div> </pre>
<p>You can either script in parallel as:</p> <p>You can either script in parallel as:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">%</span> <span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">4</span> <span class="n">python</span> <span class="n">test</span><span class="o">.</span><span class="n">py</span> <div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">%</span> <span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">4</span> <span class="n">python</span> <span class="n">test</span><span class="o">.</span><span class="n">py</span>
</pre></div> </pre></div>
</div> </div>
<p>and you should see the same output as if you had typed</p> <p>and you should see the same output as if you had typed</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">%</span> <span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">4</span> <span class="n">lmp_g</span><span class="o">++</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <pre class="literal-block">
</pre></div> % mpirun -np 4 lmp_g++ -in in.lj
</div> </pre>
<p>Note that if you leave out the 3 lines from test.py that specify Pypar <p>Note that if you leave out the 3 lines from test.py that specify PyPar
commands you will instantiate and run LAMMPS independently on each of commands you will instantiate and run LAMMPS independently on each of
the P processors specified in the mpirun command. In this case you the P processors specified in the mpirun command. In this case you
should get 4 sets of output, each showing that a LAMMPS run was made should get 4 sets of output, each showing that a LAMMPS run was made
on a single processor, instead of one set of output showing that on a single processor, instead of one set of output showing that
LAMMPS ran on 4 processors. If the 1-processor outputs occur, it LAMMPS ran on 4 processors. If the 1-processor outputs occur, it
means that Pypar is not working correctly.</p> means that PyPar is not working correctly.</p>
<p>Also note that once you import the PyPar module, Pypar initializes MPI <p>Also note that once you import the PyPar module, PyPar initializes MPI
for you, and you can use MPI calls directly in your Python script, as for you, and you can use MPI calls directly in your Python script, as
described in the Pypar documentation. The last line of your Python described in the PyPar documentation. The last line of your Python
script should be pypar.finalize(), to insure MPI is shut down script should be pypar.finalize(), to insure MPI is shut down
correctly.</p> correctly.</p>
</div> </div>
@ -661,14 +643,14 @@ Python script, as follows:</p>
the files src/library.cpp and src/library.h you will see that they the files src/library.cpp and src/library.h you will see that they
correspond one-to-one with calls you can make to the LAMMPS library correspond one-to-one with calls you can make to the LAMMPS library
from a C++ or C or Fortran program.</p> from a C++ or C or Fortran program.</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">()</span> <span class="c1"># create a LAMMPS object using the default liblammps.so library</span> <pre class="literal-block">
<span class="mi">4</span> <span class="n">optional</span> <span class="n">args</span> <span class="n">are</span> <span class="n">allowed</span><span class="p">:</span> <span class="n">name</span><span class="p">,</span> <span class="n">cmdargs</span><span class="p">,</span> <span class="n">ptr</span><span class="p">,</span> <span class="n">comm</span> lmp = lammps() # create a LAMMPS object using the default liblammps.so library
<span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">(</span><span class="n">ptr</span><span class="o">=</span><span class="n">lmpptr</span><span class="p">)</span> <span class="c1"># use lmpptr as previously created LAMMPS object</span> 4 optional args are allowed: name, cmdargs, ptr, comm
<span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">(</span><span class="n">comm</span><span class="o">=</span><span class="n">split</span><span class="p">)</span> <span class="c1"># create a LAMMPS object with a custom communicator, requires mpi4py 2.0.0 or later</span> lmp = lammps(ptr=lmpptr) # use lmpptr as previously created LAMMPS object
<span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s2">&quot;g++&quot;</span><span class="p">)</span> <span class="c1"># create a LAMMPS object using the liblammps_g++.so library</span> lmp = lammps(comm=split) # create a LAMMPS object with a custom communicator, requires mpi4py 2.0.0 or later
<span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">(</span><span class="n">name</span><span class="o">=</span><span class="s2">&quot;g++&quot;</span><span class="p">,</span><span class="n">cmdargs</span><span class="o">=</span><span class="nb">list</span><span class="p">)</span> <span class="c1"># add LAMMPS command-line args, e.g. list = [&quot;-echo&quot;,&quot;screen&quot;]</span> lmp = lammps(name=&quot;g++&quot;) # create a LAMMPS object using the liblammps_g++.so library
</pre></div> lmp = lammps(name=&quot;g++&quot;,cmdargs=list) # add LAMMPS command-line args, e.g. list = [&quot;-echo&quot;,&quot;screen&quot;]
</div> </pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp</span><span class="o">.</span><span class="n">close</span><span class="p">()</span> <span class="c1"># destroy a LAMMPS object</span> <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp</span><span class="o">.</span><span class="n">close</span><span class="p">()</span> <span class="c1"># destroy a LAMMPS object</span>
</pre></div> </pre></div>
</div> </div>
@ -677,49 +659,49 @@ from a C++ or C or Fortran program.</p>
<span class="n">lmp</span><span class="o">.</span><span class="n">command</span><span class="p">(</span><span class="n">cmd</span><span class="p">)</span> <span class="c1"># invoke a single LAMMPS command, cmd = &quot;run 100&quot;</span> <span class="n">lmp</span><span class="o">.</span><span class="n">command</span><span class="p">(</span><span class="n">cmd</span><span class="p">)</span> <span class="c1"># invoke a single LAMMPS command, cmd = &quot;run 100&quot;</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">xlo</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">extract_global</span><span class="p">(</span><span class="n">name</span><span class="p">,</span><span class="nb">type</span><span class="p">)</span> <span class="c1"># extract a global quantity</span> <pre class="literal-block">
<span class="c1"># name = &quot;boxxlo&quot;, &quot;nlocal&quot;, etc</span> xlo = lmp.extract_global(name,type) # extract a global quantity
<span class="c1"># type = 0 = int</span> # name = &quot;boxxlo&quot;, &quot;nlocal&quot;, etc
<span class="c1"># 1 = double</span> # type = 0 = int
</pre></div> # 1 = double
</div> </pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">coords</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">extract_atom</span><span class="p">(</span><span class="n">name</span><span class="p">,</span><span class="nb">type</span><span class="p">)</span> <span class="c1"># extract a per-atom quantity</span> <pre class="literal-block">
<span class="c1"># name = &quot;x&quot;, &quot;type&quot;, etc</span> coords = lmp.extract_atom(name,type) # extract a per-atom quantity
<span class="c1"># type = 0 = vector of ints</span> # name = &quot;x&quot;, &quot;type&quot;, etc
<span class="c1"># 1 = array of ints</span> # type = 0 = vector of ints
<span class="c1"># 2 = vector of doubles</span> # 1 = array of ints
<span class="c1"># 3 = array of doubles</span> # 2 = vector of doubles
</pre></div> # 3 = array of doubles
</div> </pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">eng</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">extract_compute</span><span class="p">(</span><span class="nb">id</span><span class="p">,</span><span class="n">style</span><span class="p">,</span><span class="nb">type</span><span class="p">)</span> <span class="c1"># extract value(s) from a compute</span> <pre class="literal-block">
<span class="n">v3</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">extract_fix</span><span class="p">(</span><span class="nb">id</span><span class="p">,</span><span class="n">style</span><span class="p">,</span><span class="nb">type</span><span class="p">,</span><span class="n">i</span><span class="p">,</span><span class="n">j</span><span class="p">)</span> <span class="c1"># extract value(s) from a fix</span> eng = lmp.extract_compute(id,style,type) # extract value(s) from a compute
<span class="c1"># id = ID of compute or fix</span> v3 = lmp.extract_fix(id,style,type,i,j) # extract value(s) from a fix
<span class="c1"># style = 0 = global data</span> # id = ID of compute or fix
<span class="c1"># 1 = per-atom data</span> # style = 0 = global data
<span class="c1"># 2 = local data</span> # 1 = per-atom data
<span class="c1"># type = 0 = scalar</span> # 2 = local data
<span class="c1"># 1 = vector</span> # type = 0 = scalar
<span class="c1"># 2 = array</span> # 1 = vector
<span class="c1"># i,j = indices of value in global vector or array</span> # 2 = array
</pre></div> # i,j = indices of value in global vector or array
</div> </pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">var</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">extract_variable</span><span class="p">(</span><span class="n">name</span><span class="p">,</span><span class="n">group</span><span class="p">,</span><span class="n">flag</span><span class="p">)</span> <span class="c1"># extract value(s) from a variable</span> <pre class="literal-block">
<span class="c1"># name = name of variable</span> var = lmp.extract_variable(name,group,flag) # extract value(s) from a variable
<span class="c1"># group = group ID (ignored for equal-style variables)</span> # name = name of variable
<span class="c1"># flag = 0 = equal-style variable</span> # group = group ID (ignored for equal-style variables)
<span class="c1"># 1 = atom-style variable</span> # flag = 0 = equal-style variable
</pre></div> # 1 = atom-style variable
</div> </pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">flag</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">set_variable</span><span class="p">(</span><span class="n">name</span><span class="p">,</span><span class="n">value</span><span class="p">)</span> <span class="c1"># set existing named string-style variable to value, flag = 0 if successful</span> <pre class="literal-block">
<span class="n">natoms</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">get_natoms</span><span class="p">()</span> <span class="c1"># total # of atoms as int</span> flag = lmp.set_variable(name,value) # set existing named string-style variable to value, flag = 0 if successful
<span class="n">data</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">gather_atoms</span><span class="p">(</span><span class="n">name</span><span class="p">,</span><span class="nb">type</span><span class="p">,</span><span class="n">count</span><span class="p">)</span> <span class="c1"># return atom attribute of all atoms gathered into data, ordered by atom ID</span> natoms = lmp.get_natoms() # total # of atoms as int
<span class="c1"># name = &quot;x&quot;, &quot;charge&quot;, &quot;type&quot;, etc</span> data = lmp.gather_atoms(name,type,count) # return atom attribute of all atoms gathered into data, ordered by atom ID
<span class="c1"># count = # of per-atom values, 1 or 3, etc</span> # name = &quot;x&quot;, &quot;charge&quot;, &quot;type&quot;, etc
<span class="n">lmp</span><span class="o">.</span><span class="n">scatter_atoms</span><span class="p">(</span><span class="n">name</span><span class="p">,</span><span class="nb">type</span><span class="p">,</span><span class="n">count</span><span class="p">,</span><span class="n">data</span><span class="p">)</span> <span class="c1"># scatter atom attribute of all atoms from data, ordered by atom ID</span> # count = # of per-atom values, 1 or 3, etc
<span class="c1"># name = &quot;x&quot;, &quot;charge&quot;, &quot;type&quot;, etc</span> lmp.scatter_atoms(name,type,count,data) # scatter atom attribute of all atoms from data, ordered by atom ID
<span class="c1"># count = # of per-atom values, 1 or 3, etc</span> # name = &quot;x&quot;, &quot;charge&quot;, &quot;type&quot;, etc
</pre></div> # count = # of per-atom values, 1 or 3, etc
</div> </pre>
<hr class="docutils" /> <hr class="docutils" />
<p>The lines</p> <p>The lines</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">lammps</span> <span class="k">import</span> <span class="n">lammps</span> <div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">lammps</span> <span class="k">import</span> <span class="n">lammps</span>
@ -767,8 +749,8 @@ argument.</p>
returned, which you can use via normal Python subscripting. See the returned, which you can use via normal Python subscripting. See the
extract() method in the src/atom.cpp file for a list of valid names. extract() method in the src/atom.cpp file for a list of valid names.
Again, new names could easily be added. A pointer to a vector of Again, new names could easily be added. A pointer to a vector of
doubles or integers, or a pointer to an array of doubles (double <a href="#id3"><span class="problematic" id="id4">**</span></a>) doubles or integers, or a pointer to an array of doubles (double **)
or integers (int <a href="#id5"><span class="problematic" id="id6">**</span></a>) is returned. You need to specify the appropriate or integers (int **) is returned. You need to specify the appropriate
data type via the type argument.</p> data type via the type argument.</p>
<p>For extract_compute() and extract_fix(), the global, per-atom, or <p>For extract_compute() and extract_fix(), the global, per-atom, or
local data calulated by the compute or fix can be accessed. What is local data calulated by the compute or fix can be accessed. What is
@ -824,19 +806,19 @@ consecutively ordered, no coordinates are reset.</p>
<p>The array of coordinates passed to scatter_atoms() must be a ctypes <p>The array of coordinates passed to scatter_atoms() must be a ctypes
vector of ints or doubles, allocated and initialized something like vector of ints or doubles, allocated and initialized something like
this:</p> this:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">ctypes</span> <span class="k">import</span> <span class="o">*</span> <pre class="literal-block">
<span class="n">natoms</span> <span class="o">=</span> <span class="n">lmp</span><span class="o">.</span><span class="n">get_natoms</span><span class="p">()</span> from ctypes import *
<span class="n">n3</span> <span class="o">=</span> <span class="mi">3</span><span class="o">*</span><span class="n">natoms</span> natoms = lmp.get_natoms()
<span class="n">x</span> <span class="o">=</span> <span class="p">(</span><span class="n">n3</span><span class="o">*</span><span class="n">c_double</span><span class="p">)()</span> n3 = 3*natoms
<span class="n">x</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">=</span> <span class="n">x</span> <span class="n">coord</span> <span class="n">of</span> <span class="n">atom</span> <span class="k">with</span> <span class="n">ID</span> <span class="mi">1</span> x = (n3*c_double)()
<span class="n">x</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">y</span> <span class="n">coord</span> <span class="n">of</span> <span class="n">atom</span> <span class="k">with</span> <span class="n">ID</span> <span class="mi">1</span> x[0] = x coord of atom with ID 1
<span class="n">x</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="n">z</span> <span class="n">coord</span> <span class="n">of</span> <span class="n">atom</span> <span class="k">with</span> <span class="n">ID</span> <span class="mi">1</span> x[1] = y coord of atom with ID 1
<span class="n">x</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">=</span> <span class="n">x</span> <span class="n">coord</span> <span class="n">of</span> <span class="n">atom</span> <span class="k">with</span> <span class="n">ID</span> <span class="mi">2</span> x[2] = z coord of atom with ID 1
<span class="o">...</span> x[3] = x coord of atom with ID 2
<span class="n">x</span><span class="p">[</span><span class="n">n3</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span> <span class="o">=</span> <span class="n">z</span> <span class="n">coord</span> <span class="n">of</span> <span class="n">atom</span> <span class="k">with</span> <span class="n">ID</span> <span class="n">natoms</span> ...
<span class="n">lmp</span><span class="o">.</span><span class="n">scatter_coords</span><span class="p">(</span><span class="s2">&quot;x&quot;</span><span class="p">,</span><span class="mi">1</span><span class="p">,</span><span class="mi">3</span><span class="p">,</span><span class="n">x</span><span class="p">)</span> x[n3-1] = z coord of atom with ID natoms
</pre></div> lmp.scatter_coords(&quot;x&quot;,1,3,x)
</div> </pre>
<p>Alternatively, you can just change values in the vector returned by <p>Alternatively, you can just change values in the vector returned by
gather_atoms(&#8220;x&#8221;,1,3), since it is a ctypes vector of doubles.</p> gather_atoms(&#8220;x&#8221;,1,3), since it is a ctypes vector of doubles.</p>
<hr class="docutils" /> <hr class="docutils" />
@ -915,10 +897,10 @@ capability needed by these Python scripts.</p>
open-source version of PyMol in your Python, so that you can import it open-source version of PyMol in your Python, so that you can import it
from a Python script. See the PyMol WWW pages <a class="reference external" href="http://www.pymol.org">here</a> or from a Python script. See the PyMol WWW pages <a class="reference external" href="http://www.pymol.org">here</a> or
<a class="reference external" href="http://sourceforge.net/scm/?type=svn&amp;group_id=4546">here</a> for more details:</p> <a class="reference external" href="http://sourceforge.net/scm/?type=svn&amp;group_id=4546">here</a> for more details:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span>http://www.pymol.org <pre class="literal-block">
http://sourceforge.net/scm/?type=svn&amp;group_id=4546 <a class="reference external" href="http://www.pymol.org">http://www.pymol.org</a>
</pre></div> <a class="reference external" href="http://sourceforge.net/scm/?type=svn&amp;group_id=4546">http://sourceforge.net/scm/?type=svn&amp;group_id=4546</a>
</div> </pre>
<p>The latter link is to the open-source version.</p> <p>The latter link is to the open-source version.</p>
<p>Note that for VMD, you need a fairly current version (1.8.7 works for <p>Note that for VMD, you need a fairly current version (1.8.7 works for
me) and there are some lines in the pizza/vmd.py script for 4 PIZZA me) and there are some lines in the pizza/vmd.py script for 4 PIZZA

130
doc/html/Section_start.html
View File

@ -173,10 +173,10 @@ experienced users.</p>
<p>When you download a LAMMPS tarball you will need to unzip and untar <p>When you download a LAMMPS tarball you will need to unzip and untar
the downloaded file with the following commands, after placing the the downloaded file with the following commands, after placing the
tarball in an appropriate directory.</p> tarball in an appropriate directory.</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">gunzip</span> <span class="n">lammps</span><span class="o">*.</span><span class="n">tar</span><span class="o">.</span><span class="n">gz</span> <pre class="literal-block">
<span class="n">tar</span> <span class="n">xvf</span> <span class="n">lammps</span><span class="o">*.</span><span class="n">tar</span> gunzip lammps*.tar.gz
</pre></div> tar xvf lammps*.tar
</div> </pre>
<p>This will create a LAMMPS directory containing two files and several <p>This will create a LAMMPS directory containing two files and several
sub-directories:</p> sub-directories:</p>
<table border="1" class="docutils"> <table border="1" class="docutils">
@ -315,13 +315,13 @@ it will be never be touched by any LAMMPS updates.</p>
a list of available choices from src/MAKE and all of its a list of available choices from src/MAKE and all of its
sub-directories. If one of those has the options you want or is the sub-directories. If one of those has the options you want or is the
machine you want, you can type a command like:</p> machine you want, you can type a command like:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">make</span> <span class="n">mpi</span> <pre class="literal-block">
<span class="ow">or</span> make mpi
<span class="n">make</span> <span class="n">serial_icc</span> or
<span class="ow">or</span> make serial_icc
<span class="n">gmake</span> <span class="n">mac</span> or
</pre></div> gmake mac
</div> </pre>
<p>Note that the corresponding Makefile.machine can exist in src/MAKE or <p>Note that the corresponding Makefile.machine can exist in src/MAKE or
any of its sub-directories. If a file with the same name appears in any of its sub-directories. If a file with the same name appears in
multiple places (not a good idea), the order they are used is as multiple places (not a good idea), the order they are used is as
@ -362,13 +362,13 @@ then you should list them as part of the LIB variable. You should
not need to do this if you use mpicxx.</p> not need to do this if you use mpicxx.</p>
<p>The DEPFLAGS setting is what triggers the C++ compiler to create a <p>The DEPFLAGS setting is what triggers the C++ compiler to create a
dependency list for a source file. This speeds re-compilation when dependency list for a source file. This speeds re-compilation when
source (<em>.cpp) or header (</em>.h) files are edited. Some compilers do source (*.cpp) or header (*.h) files are edited. Some compilers do
not support dependency file creation, or may use a different switch not support dependency file creation, or may use a different switch
than -D. GNU g++ and Intel icc works with -D. If your compiler can&#8217;t than -D. GNU g++ and Intel icc works with -D. If your compiler can&#8217;t
create dependency files, then you&#8217;ll need to create a Makefile.foo create dependency files, then you&#8217;ll need to create a Makefile.foo
patterned after Makefile.storm, which uses different rules that do not patterned after Makefile.storm, which uses different rules that do not
involve dependency files. Note that when you build LAMMPS for the involve dependency files. Note that when you build LAMMPS for the
first time on a new platform, a long list of <a href="#id5"><span class="problematic" id="id6">*</span></a>.d files will be printed first time on a new platform, a long list of *.d files will be printed
out rapidly. This is not an error; it is the Makefile doing its out rapidly. This is not an error; it is the Makefile doing its
normal creation of dependencies.</p> normal creation of dependencies.</p>
<p><strong>Step 4</strong></p> <p><strong>Step 4</strong></p>
@ -598,7 +598,7 @@ faster, depending on how many cores your compilation machine has. N
is the number of cores the build runs on.</p> is the number of cores the build runs on.</p>
<p>You should get the executable lmp_foo when the build is complete.</p> <p>You should get the executable lmp_foo when the build is complete.</p>
<hr class="docutils" /> <hr class="docutils" />
<p id="start-2-3"><a href="#id7"><span class="problematic" id="id8">**</span></a><em>Errors that can occur when making LAMMPS:</em>**</p> <p id="start-2-3"><a href="#id5"><span class="problematic" id="id6">**</span></a><em>Errors that can occur when making LAMMPS:</em>**</p>
<div class="admonition note"> <div class="admonition note">
<p class="first admonition-title">Note</p> <p class="first admonition-title">Note</p>
<p class="last">If an error occurs when building LAMMPS, the compiler or linker <p class="last">If an error occurs when building LAMMPS, the compiler or linker
@ -632,17 +632,17 @@ is undefined&#8217;, then your machine does not support &#8220;long long&#8221;
integers. Try using the -DLAMMPS_LONGLONG_TO_LONG setting described integers. Try using the -DLAMMPS_LONGLONG_TO_LONG setting described
above in Step 4.</p> above in Step 4.</p>
<hr class="docutils" /> <hr class="docutils" />
<p id="start-2-4"><a href="#id9"><span class="problematic" id="id10">**</span></a><em>Additional build tips:</em>**</p> <p id="start-2-4"><a href="#id7"><span class="problematic" id="id8">**</span></a><em>Additional build tips:</em>**</p>
<ol class="arabic simple"> <ol class="arabic simple">
<li>Building LAMMPS for multiple platforms.</li> <li>Building LAMMPS for multiple platforms.</li>
</ol> </ol>
<p>You can make LAMMPS for multiple platforms from the same src <p>You can make LAMMPS for multiple platforms from the same src
directory. Each target creates its own object sub-directory called directory. Each target creates its own object sub-directory called
Obj_target where it stores the system-specific <a href="#id11"><span class="problematic" id="id12">*</span></a>.o files.</p> Obj_target where it stores the system-specific *.o files.</p>
<ol class="arabic simple" start="2"> <ol class="arabic simple" start="2">
<li>Cleaning up.</li> <li>Cleaning up.</li>
</ol> </ol>
<p>Typing &#8220;make clean-all&#8221; or &#8220;make clean-machine&#8221; will delete <a href="#id13"><span class="problematic" id="id14">*</span></a>.o object <p>Typing &#8220;make clean-all&#8221; or &#8220;make clean-machine&#8221; will delete *.o object
files created when LAMMPS is built, for either all builds or for a files created when LAMMPS is built, for either all builds or for a
particular machine.</p> particular machine.</p>
<p>(3) Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or <p>(3) Changing the LAMMPS size limits via -DLAMMPS_SMALLBIG or
@ -686,11 +686,11 @@ basis is limited by 4-byte integer storage to 2^31 atoms per processor
a problem would have a huge per-processor memory footprint due to a problem would have a huge per-processor memory footprint due to
neighbor lists and would run very slowly in terms of CPU secs/timestep.</p> neighbor lists and would run very slowly in terms of CPU secs/timestep.</p>
<hr class="docutils" /> <hr class="docutils" />
<p id="start-2-5"><a href="#id15"><span class="problematic" id="id16">**</span></a><em>Building for a Mac:</em>**</p> <p id="start-2-5"><a href="#id9"><span class="problematic" id="id10">**</span></a><em>Building for a Mac:</em>**</p>
<p>OS X is BSD Unix, so it should just work. See the <p>OS X is BSD Unix, so it should just work. See the
src/MAKE/MACHINES/Makefile.mac and Makefile.mac_mpi files.</p> src/MAKE/MACHINES/Makefile.mac and Makefile.mac_mpi files.</p>
<hr class="docutils" /> <hr class="docutils" />
<p id="start-2-6"><a href="#id17"><span class="problematic" id="id18">**</span></a><em>Building for Windows:</em>**</p> <p id="start-2-6"><a href="#id11"><span class="problematic" id="id12">**</span></a><em>Building for Windows:</em>**</p>
<p>The LAMMPS download page has an option to download both a serial and <p>The LAMMPS download page has an option to download both a serial and
parallel pre-built Windows executable. See the <a class="reference internal" href="#start-6"><span class="std std-ref">Running LAMMPS</span></a> section for instructions on running these executables parallel pre-built Windows executable. See the <a class="reference internal" href="#start-6"><span class="std std-ref">Running LAMMPS</span></a> section for instructions on running these executables
on a Windows box.</p> on a Windows box.</p>
@ -725,7 +725,7 @@ tool which can be used to install/un-install packages and build the
auxiliary libraries which some of them use. It can also auto-edit a auxiliary libraries which some of them use. It can also auto-edit a
Makefile.machine to add settings needed by some packages.</p> Makefile.machine to add settings needed by some packages.</p>
<hr class="docutils" /> <hr class="docutils" />
<p id="start-3-1"><a href="#id19"><span class="problematic" id="id20">**</span></a><em>Package basics:</em>**</p> <p id="start-3-1"><a href="#id13"><span class="problematic" id="id14">**</span></a><em>Package basics:</em>**</p>
<p>The source code for LAMMPS is structured as a set of core files which <p>The source code for LAMMPS is structured as a set of core files which
are always included, plus optional packages. Packages are groups of are always included, plus optional packages. Packages are groups of
files that enable a specific set of features. For example, force files that enable a specific set of features. For example, force
@ -742,9 +742,9 @@ package, you must have built LAMMPS with that package, else you will
get an error that the style is invalid or the command is unknown. get an error that the style is invalid or the command is unknown.
Every command&#8217;s doc page specfies if it is part of a package. You can Every command&#8217;s doc page specfies if it is part of a package. You can
also type</p> also type</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_machine</span> <span class="o">-</span><span class="n">h</span> <pre class="literal-block">
</pre></div> lmp_machine -h
</div> </pre>
<p>to run your executable with the optional <a class="reference internal" href="#start-7"><span class="std std-ref">-h command-line switch</span></a> for &#8220;help&#8221;, which will simply list the styles and <p>to run your executable with the optional <a class="reference internal" href="#start-7"><span class="std std-ref">-h command-line switch</span></a> for &#8220;help&#8221;, which will simply list the styles and
commands known to your executable, and immediately exit.</p> commands known to your executable, and immediately exit.</p>
<p>There are two kinds of packages in LAMMPS, standard and user packages. <p>There are two kinds of packages in LAMMPS, standard and user packages.
@ -768,7 +768,7 @@ Information on how to submit additions you make to LAMMPS as single
files or either a standard or user-contributed package are given in files or either a standard or user-contributed package are given in
<a class="reference internal" href="Section_modify.html#mod-15"><span class="std std-ref">this section</span></a> of the documentation.</p> <a class="reference internal" href="Section_modify.html#mod-15"><span class="std std-ref">this section</span></a> of the documentation.</p>
<hr class="docutils" /> <hr class="docutils" />
<p id="start-3-2"><a href="#id21"><span class="problematic" id="id22">**</span></a><em>Including/excluding packages:</em>**</p> <p id="start-3-2"><a href="#id15"><span class="problematic" id="id16">**</span></a><em>Including/excluding packages:</em>**</p>
<p>To use (or not use) a package you must include it (or exclude it) <p>To use (or not use) a package you must include it (or exclude it)
before building LAMMPS. From the src directory, this is typically as before building LAMMPS. From the src directory, this is typically as
simple as:</p> simple as:</p>
@ -837,7 +837,7 @@ sub-directory. Typing &#8220;make package-diff&#8221; lists all differences
between these files. Again, type &#8220;make package&#8221; to see all of the between these files. Again, type &#8220;make package&#8221; to see all of the
package-related make options.</p> package-related make options.</p>
<hr class="docutils" /> <hr class="docutils" />
<p id="start-3-3"><a href="#id23"><span class="problematic" id="id24">**</span></a><em>Packages that require extra libraries:</em>**</p> <p id="start-3-3"><a href="#id17"><span class="problematic" id="id18">**</span></a><em>Packages that require extra libraries:</em>**</p>
<p>A few of the standard and user packages require additional auxiliary <p>A few of the standard and user packages require additional auxiliary
libraries. Many of them are provided with LAMMPS, in which case they libraries. Many of them are provided with LAMMPS, in which case they
must be compiled first, before LAMMPS is built, if you wish to include must be compiled first, before LAMMPS is built, if you wish to include
@ -908,7 +908,7 @@ needed soft links. Type &#8220;python install.py&#8221; for further instruction
or settings in the lib/package/Makefile.lammps files are not correct, or settings in the lib/package/Makefile.lammps files are not correct,
the LAMMPS build will typically fail.</p> the LAMMPS build will typically fail.</p>
<hr class="docutils" /> <hr class="docutils" />
<p id="start-3-4"><a href="#id25"><span class="problematic" id="id26">**</span></a><em>Packages that require Makefile.machine settings</em>**</p> <p id="start-3-4"><a href="#id19"><span class="problematic" id="id20">**</span></a><em>Packages that require Makefile.machine settings</em>**</p>
<p>A few packages require specific settings in Makefile.machine, to <p>A few packages require specific settings in Makefile.machine, to
either build or use the package effectively. These are the either build or use the package effectively. These are the
USER-INTEL, KOKKOS, USER-OMP, and OPT packages, used for accelerating USER-INTEL, KOKKOS, USER-OMP, and OPT packages, used for accelerating
@ -1081,7 +1081,7 @@ LAMMPS to other codes. See <a class="reference internal" href="Section_python.h
more info on wrapping and running LAMMPS from Python.</p> more info on wrapping and running LAMMPS from Python.</p>
<div class="section" id="static-library"> <div class="section" id="static-library">
<h3>2.5.1. <strong>Static library:</strong></h3> <h3>2.5.1. <strong>Static library:</strong></h3>
<p>To build LAMMPS as a static library (<a href="#id27"><span class="problematic" id="id28">*</span></a>.a file on Linux), type</p> <p>To build LAMMPS as a static library (*.a file on Linux), type</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">make</span> <span class="n">foo</span> <span class="n">mode</span><span class="o">=</span><span class="n">lib</span> <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">make</span> <span class="n">foo</span> <span class="n">mode</span><span class="o">=</span><span class="n">lib</span>
</pre></div> </pre></div>
</div> </div>
@ -1095,7 +1095,7 @@ point to the most recently built static library.</p>
</div> </div>
<div class="section" id="shared-library"> <div class="section" id="shared-library">
<h3>2.5.2. <strong>Shared library:</strong></h3> <h3>2.5.2. <strong>Shared library:</strong></h3>
<p>To build LAMMPS as a shared library (<a href="#id29"><span class="problematic" id="id30">*</span></a>.so file on Linux), which can be <p>To build LAMMPS as a shared library (*.so file on Linux), which can be
dynamically loaded, e.g. from Python, type</p> dynamically loaded, e.g. from Python, type</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">make</span> <span class="n">foo</span> <span class="n">mode</span><span class="o">=</span><span class="n">shlib</span> <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">make</span> <span class="n">foo</span> <span class="n">mode</span><span class="o">=</span><span class="n">shlib</span>
</pre></div> </pre></div>
@ -1122,18 +1122,18 @@ of the auxiliary library. The build instructions for the library
should tell you how to do this.</p> should tell you how to do this.</p>
<p>Here is an example of such errors when the system FFTW or provided <p>Here is an example of such errors when the system FFTW or provided
lib/colvars library have not been built as shared libraries:</p> lib/colvars library have not been built as shared libraries:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span>/usr/bin/ld: /usr/local/lib/libfftw3.a(mapflags.o): relocation <pre class="literal-block">
R_X86_64_32 against `.rodata&#39; can not be used when making a shared /usr/bin/ld: /usr/local/lib/libfftw3.a(mapflags.o): relocation
R_X86_64_32 against '.rodata' can not be used when making a shared
object; recompile with -fPIC object; recompile with -fPIC
/usr/local/lib/libfftw3.a: could not read symbols: Bad value /usr/local/lib/libfftw3.a: could not read symbols: Bad value
</pre></div> </pre>
</div> <pre class="literal-block">
<div class="highlight-default"><div class="highlight"><pre><span></span>/usr/bin/ld: ../../lib/colvars/libcolvars.a(colvarmodule.o): /usr/bin/ld: ../../lib/colvars/libcolvars.a(colvarmodule.o):
relocation R_X86_64_32 against `__pthread_key_create&#39; can not be used relocation R_X86_64_32 against '__pthread_key_create' can not be used
when making a shared object; recompile with -fPIC when making a shared object; recompile with -fPIC
../../lib/colvars/libcolvars.a: error adding symbols: Bad value ../../lib/colvars/libcolvars.a: error adding symbols: Bad value
</pre></div> </pre>
</div>
<p>As an example, here is how to build and install the <a class="reference external" href="http://www-unix.mcs.anl.gov/mpi">MPICH library</a>, a popular open-source version of MPI, distributed by <p>As an example, here is how to build and install the <a class="reference external" href="http://www-unix.mcs.anl.gov/mpi">MPICH library</a>, a popular open-source version of MPI, distributed by
Argonne National Labs, as a shared library in the default Argonne National Labs, as a shared library in the default
/usr/local/lib location:</p> /usr/local/lib location:</p>
@ -1157,9 +1157,9 @@ current version of the shared library is always available to programs
that use it.</p> that use it.</p>
<p>For the csh or tcsh shells, you would add something like this to your <p>For the csh or tcsh shells, you would add something like this to your
~/.cshrc file:</p> ~/.cshrc file:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span>setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src <pre class="literal-block">
</pre></div> setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:/home/sjplimp/lammps/src
</div> </pre>
</div> </div>
<div class="section" id="calling-the-lammps-library"> <div class="section" id="calling-the-lammps-library">
<h3>2.5.4. <strong>Calling the LAMMPS library:</strong></h3> <h3>2.5.4. <strong>Calling the LAMMPS library:</strong></h3>
@ -1188,20 +1188,20 @@ interface and how to extend it for your needs.</p>
<span id="start-6"></span><h2>2.6. Running LAMMPS</h2> <span id="start-6"></span><h2>2.6. Running LAMMPS</h2>
<p>By default, LAMMPS runs by reading commands from standard input. Thus <p>By default, LAMMPS runs by reading commands from standard input. Thus
if you run the LAMMPS executable by itself, e.g.</p> if you run the LAMMPS executable by itself, e.g.</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_linux</span> <pre class="literal-block">
</pre></div> lmp_linux
</div> </pre>
<p>it will simply wait, expecting commands from the keyboard. Typically <p>it will simply wait, expecting commands from the keyboard. Typically
you should put commands in an input script and use I/O redirection, you should put commands in an input script and use I/O redirection,
e.g.</p> e.g.</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_linux</span> <span class="o">&lt;</span> <span class="ow">in</span><span class="o">.</span><span class="n">file</span> <pre class="literal-block">
</pre></div> lmp_linux &lt; in.file
</div> </pre>
<p>For parallel environments this should also work. If it does not, use <p>For parallel environments this should also work. If it does not, use
the &#8216;-in&#8217; command-line switch, e.g.</p> the &#8216;-in&#8217; command-line switch, e.g.</p>
<div class="highlight-default"><div class="highlight"><pre><span></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">file</span> <pre class="literal-block">
</pre></div> lmp_linux -in in.file
</div> </pre>
<p><a class="reference internal" href="Section_commands.html"><span class="doc">This section</span></a> describes how input scripts are <p><a class="reference internal" href="Section_commands.html"><span class="doc">This section</span></a> describes how input scripts are
structured and what commands they contain.</p> structured and what commands they contain.</p>
<p>You can test LAMMPS on any of the sample inputs provided in the <p>You can test LAMMPS on any of the sample inputs provided in the
@ -1210,13 +1210,13 @@ outputs are named log.*.name.P where name is a machine and P is the
number of processors it was run on.</p> number of processors it was run on.</p>
<p>Here is how you might run a standard Lennard-Jones benchmark on a <p>Here is how you might run a standard Lennard-Jones benchmark on a
Linux box, using mpirun to launch a parallel job:</p> Linux box, using mpirun to launch a parallel job:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">cd</span> <span class="n">src</span> <pre class="literal-block">
<span class="n">make</span> <span class="n">linux</span> cd src
<span class="n">cp</span> <span class="n">lmp_linux</span> <span class="o">../</span><span class="n">bench</span> make linux
<span class="n">cd</span> <span class="o">../</span><span class="n">bench</span> cp lmp_linux ../bench
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">4</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">lj</span> cd ../bench
</pre></div> mpirun -np 4 lmp_linux -in in.lj
</div> </pre>
<p>See <a class="reference external" href="http://lammps.sandia.gov/bench.html">this page</a> for timings for this and the other benchmarks on <p>See <a class="reference external" href="http://lammps.sandia.gov/bench.html">this page</a> for timings for this and the other benchmarks on
various platforms. Note that some of the example scripts require various platforms. Note that some of the example scripts require
LAMMPS to be built with one or more of its optional packages.</p> LAMMPS to be built with one or more of its optional packages.</p>
@ -1256,7 +1256,7 @@ in.lj&#8221;, replacing in.lj with the name of your LAMMPS input script.</li>
matter what you type).</li> matter what you type).</li>
<li>In this mode, output may not immediately show up on the screen, so if <li>In this mode, output may not immediately show up on the screen, so if
your input script takes a long time to execute, you may need to be your input script takes a long time to execute, you may need to be
patient before the output shows up. :l Alternatively, you can still patient before the output shows up. Alternatively, you can still
use this executable to run on a single processor by typing something use this executable to run on a single processor by typing something
like: &#8220;lmp_win_mpi -in in.lj&#8221;.</li> like: &#8220;lmp_win_mpi -in in.lj&#8221;.</li>
</ul> </ul>
@ -1309,10 +1309,10 @@ letter abbreviation can be used:</p>
<li>-v or -var</li> <li>-v or -var</li>
</ul> </ul>
<p>For example, lmp_ibm might be launched as follows:</p> <p>For example, lmp_ibm might be launched as follows:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">16</span> <span class="n">lmp_ibm</span> <span class="o">-</span><span class="n">v</span> <span class="n">f</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span> <span class="o">-</span><span class="n">l</span> <span class="n">my</span><span class="o">.</span><span class="n">log</span> <span class="o">-</span><span class="n">sc</span> <span class="n">none</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">alloy</span> <pre class="literal-block">
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">16</span> <span class="n">lmp_ibm</span> <span class="o">-</span><span class="n">var</span> <span class="n">f</span> <span class="n">tmp</span><span class="o">.</span><span class="n">out</span> <span class="o">-</span><span class="n">log</span> <span class="n">my</span><span class="o">.</span><span class="n">log</span> <span class="o">-</span><span class="n">screen</span> <span class="n">none</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">alloy</span> mpirun -np 16 lmp_ibm -v f tmp.out -l my.log -sc none -in in.alloy
</pre></div> mpirun -np 16 lmp_ibm -var f tmp.out -log my.log -screen none -in in.alloy
</div> </pre>
<p>Here are the details on the options:</p> <p>Here are the details on the options:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">-</span><span class="n">echo</span> <span class="n">style</span> <div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">-</span><span class="n">echo</span> <span class="n">style</span>
</pre></div> </pre></div>
@ -1395,11 +1395,11 @@ are intended for computational work like running LAMMPS. By default
Ng = 1 and Ns is not set.</p> Ng = 1 and Ns is not set.</p>
<p>Depending on which flavor of MPI you are running, LAMMPS will look for <p>Depending on which flavor of MPI you are running, LAMMPS will look for
one of these 3 environment variables</p> one of these 3 environment variables</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">SLURM_LOCALID</span> <span class="p">(</span><span class="n">various</span> <span class="n">MPI</span> <span class="n">variants</span> <span class="n">compiled</span> <span class="k">with</span> <span class="n">SLURM</span> <span class="n">support</span><span class="p">)</span> <pre class="literal-block">
<span class="n">MV2_COMM_WORLD_LOCAL_RANK</span> <span class="p">(</span><span class="n">Mvapich</span><span class="p">)</span> SLURM_LOCALID (various MPI variants compiled with SLURM support)
<span class="n">OMPI_COMM_WORLD_LOCAL_RANK</span> <span class="p">(</span><span class="n">OpenMPI</span><span class="p">)</span> MV2_COMM_WORLD_LOCAL_RANK (Mvapich)
</pre></div> OMPI_COMM_WORLD_LOCAL_RANK (OpenMPI)
</div> </pre>
<p>which are initialized by the &#8220;srun&#8221;, &#8220;mpirun&#8221; or &#8220;mpiexec&#8221; commands. <p>which are initialized by the &#8220;srun&#8221;, &#8220;mpirun&#8221; or &#8220;mpiexec&#8221; commands.
The environment variable setting for each MPI rank is used to assign a The environment variable setting for each MPI rank is used to assign a
unique GPU ID to the MPI task.</p> unique GPU ID to the MPI task.</p>

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@ -218,7 +218,7 @@ own sub-directories with their own Makefiles.</p>
<li><a class="reference internal" href="#polybond"><span class="std std-ref">polymer bonding</span></a></li> <li><a class="reference internal" href="#polybond"><span class="std std-ref">polymer bonding</span></a></li>
<li><span class="xref std std-ref">pymol_asphere</span></li> <li><span class="xref std std-ref">pymol_asphere</span></li>
<li><a class="reference internal" href="#pythontools"><span class="std std-ref">python</span></a></li> <li><a class="reference internal" href="#pythontools"><span class="std std-ref">python</span></a></li>
<li><a class="reference internal" href="#reax"><span class="std std-ref">reax</span></a></li> <li><a class="reference internal" href="#reax-tool"><span class="std std-ref">reax</span></a></li>
<li><a class="reference internal" href="#restart"><span class="std std-ref">restart2data</span></a></li> <li><a class="reference internal" href="#restart"><span class="std std-ref">restart2data</span></a></li>
<li><a class="reference internal" href="#vim"><span class="std std-ref">vim</span></a></li> <li><a class="reference internal" href="#vim"><span class="std std-ref">vim</span></a></li>
<li><a class="reference internal" href="#xmgrace"><span class="std std-ref">xmgrace</span></a></li> <li><a class="reference internal" href="#xmgrace"><span class="std std-ref">xmgrace</span></a></li>
@ -289,9 +289,9 @@ at: <a class="reference external" href="https://github.com/colvars/colvars/issue
<p>abf_integrate:</p> <p>abf_integrate:</p>
<p>MC-based integration of multidimensional free energy gradient <p>MC-based integration of multidimensional free energy gradient
Version 20110511</p> Version 20110511</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Syntax</span><span class="p">:</span> <span class="o">./</span><span class="n">abf_integrate</span> <span class="o">&lt;</span> <span class="n">filename</span> <span class="o">&gt;</span> <span class="p">[</span><span class="o">-</span><span class="n">n</span> <span class="o">&lt;</span> <span class="n">nsteps</span> <span class="o">&gt;</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">t</span> <span class="o">&lt;</span> <span class="n">temp</span> <span class="o">&gt;</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">m</span> <span class="p">[</span><span class="mi">0</span><span class="o">|</span><span class="mi">1</span><span class="p">]</span> <span class="p">(</span><span class="n">metadynamics</span><span class="p">)]</span> <span class="p">[</span><span class="o">-</span><span class="n">h</span> <span class="o">&lt;</span> <span class="n">hill_height</span> <span class="o">&gt;</span><span class="p">]</span> <span class="p">[</span><span class="o">-</span><span class="n">f</span> <span class="o">&lt;</span> <span class="n">variable_hill_factor</span> <span class="o">&gt;</span><span class="p">]</span> <pre class="literal-block">
</pre></div> Syntax: ./abf_integrate &lt; filename &gt; [-n &lt; nsteps &gt;] [-t &lt; temp &gt;] [-m [0|1] (metadynamics)] [-h &lt; hill_height &gt;] [-f &lt; variable_hill_factor &gt;]
</div> </pre>
<p>The LAMMPS interface to the colvars collective variable library, as <p>The LAMMPS interface to the colvars collective variable library, as
well as these tools, were created by Axel Kohlmeyer (akohlmey at well as these tools, were created by Axel Kohlmeyer (akohlmey at
gmail.com) at ICTP, Italy.</p> gmail.com) at ICTP, Italy.</p>
@ -419,7 +419,7 @@ Greathouse at Sandia (jagreat at sandia.gov).</p>
<div class="section" id="lmp2cfg-tool"> <div class="section" id="lmp2cfg-tool">
<span id="cfg"></span><h2>9.17. lmp2cfg tool</h2> <span id="cfg"></span><h2>9.17. lmp2cfg tool</h2>
<p>The lmp2cfg sub-directory contains a tool for converting LAMMPS output <p>The lmp2cfg sub-directory contains a tool for converting LAMMPS output
files into a series of <a href="#id1"><span class="problematic" id="id2">*</span></a>.cfg files which can be read into the files into a series of *.cfg files which can be read into the
<a class="reference external" href="http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</a> visualizer. See <a class="reference external" href="http://mt.seas.upenn.edu/Archive/Graphics/A">AtomEye</a> visualizer. See
the README file for more information.</p> the README file for more information.</p>
<p>This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).</p> <p>This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).</p>
@ -538,7 +538,7 @@ README for more info on Pizza.py and how to use these scripts.</p>
<hr class="docutils" /> <hr class="docutils" />
</div> </div>
<div class="section" id="reax-tool"> <div class="section" id="reax-tool">
<span id="reax"></span><h2>9.27. reax tool</h2> <span id="id4"></span><h2>9.27. reax tool</h2>
<p>The reax sub-directory contains stand-alond codes that can <p>The reax sub-directory contains stand-alond codes that can
post-process the output of the <a class="reference internal" href="fix_reax_bonds.html"><span class="doc">fix reax/bonds</span></a> post-process the output of the <a class="reference internal" href="fix_reax_bonds.html"><span class="doc">fix reax/bonds</span></a>
command from a LAMMPS simulation using <a class="reference internal" href="pair_reax.html"><span class="doc">ReaxFF</span></a>. See command from a LAMMPS simulation using <a class="reference internal" href="pair_reax.html"><span class="doc">ReaxFF</span></a>. See

26
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@ -202,11 +202,11 @@ attention to 3 settings in this makefile.</p>
<p>See lib/gpu/Makefile.linux.double for examples of the ARCH settings <p>See lib/gpu/Makefile.linux.double for examples of the ARCH settings
for different GPU choices, e.g. Fermi vs Kepler. It also lists the for different GPU choices, e.g. Fermi vs Kepler. It also lists the
possible precision settings:</p> possible precision settings:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">CUDA_PREC</span> <span class="o">=</span> <span class="o">-</span><span class="n">D_SINGLE_SINGLE</span> <span class="c1"># single precision for all calculations</span> <pre class="literal-block">
<span class="n">CUDA_PREC</span> <span class="o">=</span> <span class="o">-</span><span class="n">D_DOUBLE_DOUBLE</span> <span class="c1"># double precision for all calculations</span> CUDA_PREC = -D_SINGLE_SINGLE # single precision for all calculations
<span class="n">CUDA_PREC</span> <span class="o">=</span> <span class="o">-</span><span class="n">D_SINGLE_DOUBLE</span> <span class="c1"># accumulation of forces, etc, in double</span> CUDA_PREC = -D_DOUBLE_DOUBLE # double precision for all calculations
</pre></div> CUDA_PREC = -D_SINGLE_DOUBLE # accumulation of forces, etc, in double
</div> </pre>
<p>The last setting is the mixed mode referred to above. Note that your <p>The last setting is the mixed mode referred to above. Note that your
GPU must support double precision to use either the 2nd or 3rd of GPU must support double precision to use either the 2nd or 3rd of
these settings.</p> these settings.</p>
@ -253,11 +253,11 @@ shared by 4 MPI tasks.</p>
which will automatically append &#8220;gpu&#8221; to styles that support it. Use which will automatically append &#8220;gpu&#8221; to styles that support it. Use
the &#8220;-pk gpu Ng&#8221; <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a> to the &#8220;-pk gpu Ng&#8221; <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a> to
set Ng = # of GPUs/node to use.</p> set Ng = # of GPUs/node to use.</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_machine</span> <span class="o">-</span><span class="n">sf</span> <span class="n">gpu</span> <span class="o">-</span><span class="n">pk</span> <span class="n">gpu</span> <span class="mi">1</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="c1"># 1 MPI task uses 1 GPU</span> <pre class="literal-block">
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">12</span> <span class="n">lmp_machine</span> <span class="o">-</span><span class="n">sf</span> <span class="n">gpu</span> <span class="o">-</span><span class="n">pk</span> <span class="n">gpu</span> <span class="mi">2</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="c1"># 12 MPI tasks share 2 GPUs on a single 16-core (or whatever) node</span> lmp_machine -sf gpu -pk gpu 1 -in in.script # 1 MPI task uses 1 GPU
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">48</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">12</span> <span class="n">lmp_machine</span> <span class="o">-</span><span class="n">sf</span> <span class="n">gpu</span> <span class="o">-</span><span class="n">pk</span> <span class="n">gpu</span> <span class="mi">2</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="c1"># ditto on 4 16-core nodes</span> mpirun -np 12 lmp_machine -sf gpu -pk gpu 2 -in in.script # 12 MPI tasks share 2 GPUs on a single 16-core (or whatever) node
</pre></div> mpirun -np 48 -ppn 12 lmp_machine -sf gpu -pk gpu 2 -in in.script # ditto on 4 16-core nodes
</div> </pre>
<p>Note that if the &#8220;-sf gpu&#8221; switch is used, it also issues a default <p>Note that if the &#8220;-sf gpu&#8221; switch is used, it also issues a default
<a class="reference internal" href="package.html"><span class="doc">package gpu 1</span></a> command, which sets the number of <a class="reference internal" href="package.html"><span class="doc">package gpu 1</span></a> command, which sets the number of
GPUs/node to 1.</p> GPUs/node to 1.</p>
@ -276,9 +276,9 @@ GPU package pair styles.</p>
and use of multiple MPI tasks/GPU is the same.</p> and use of multiple MPI tasks/GPU is the same.</p>
<p>Use the <a class="reference internal" href="suffix.html"><span class="doc">suffix gpu</span></a> command, or you can explicitly add an <p>Use the <a class="reference internal" href="suffix.html"><span class="doc">suffix gpu</span></a> command, or you can explicitly add an
&#8220;gpu&#8221; suffix to individual styles in your input script, e.g.</p> &#8220;gpu&#8221; suffix to individual styles in your input script, e.g.</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">gpu</span> <span class="mf">2.5</span> <pre class="literal-block">
</pre></div> pair_style lj/cut/gpu 2.5
</div> </pre>
<p>You must also use the <a class="reference internal" href="package.html"><span class="doc">package gpu</span></a> command to enable the <p>You must also use the <a class="reference internal" href="package.html"><span class="doc">package gpu</span></a> command to enable the
GPU package, unless the &#8220;-sf gpu&#8221; or &#8220;-pk gpu&#8221; <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switches</span></a> were used. It specifies the GPU package, unless the &#8220;-sf gpu&#8221; or &#8220;-pk gpu&#8221; <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switches</span></a> were used. It specifies the
number of GPUs/node to use, as well as other options.</p> number of GPUs/node to use, as well as other options.</p>

46
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@ -268,30 +268,30 @@ this information can normally be obtained with:</p>
</div> </div>
<p>Several example Makefiles for building with the Intel compiler are <p>Several example Makefiles for building with the Intel compiler are
included with LAMMPS in the src/MAKE/OPTIONS/ directory:</p> included with LAMMPS in the src/MAKE/OPTIONS/ directory:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Makefile</span><span class="o">.</span><span class="n">intel_cpu_intelmpi</span> <span class="c1"># Intel Compiler, Intel MPI, No Offload</span> <pre class="literal-block">
<span class="n">Makefile</span><span class="o">.</span><span class="n">knl</span> <span class="c1"># Intel Compiler, Intel MPI, No Offload</span> Makefile.intel_cpu_intelmpi # Intel Compiler, Intel MPI, No Offload
<span class="n">Makefile</span><span class="o">.</span><span class="n">intel_cpu_mpich</span> <span class="c1"># Intel Compiler, MPICH, No Offload</span> Makefile.knl # Intel Compiler, Intel MPI, No Offload
<span class="n">Makefile</span><span class="o">.</span><span class="n">intel_cpu_openpmi</span> <span class="c1"># Intel Compiler, OpenMPI, No Offload</span> Makefile.intel_cpu_mpich # Intel Compiler, MPICH, No Offload
<span class="n">Makefile</span><span class="o">.</span><span class="n">intel_coprocessor</span> <span class="c1"># Intel Compiler, Intel MPI, Offload</span> Makefile.intel_cpu_openpmi # Intel Compiler, OpenMPI, No Offload
</pre></div> Makefile.intel_coprocessor # Intel Compiler, Intel MPI, Offload
</div> </pre>
<p>Makefile.knl is identical to Makefile.intel_cpu_intelmpi except that <p>Makefile.knl is identical to Makefile.intel_cpu_intelmpi except that
it explicitly specifies that vectorization should be for Intel it explicitly specifies that vectorization should be for Intel
Xeon Phi x200 processors making it easier to cross-compile. For Xeon Phi x200 processors making it easier to cross-compile. For
users with recent installations of Intel Parallel Studio, the users with recent installations of Intel Parallel Studio, the
process can be as simple as:</p> process can be as simple as:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">user</span><span class="o">-</span><span class="n">intel</span> <pre class="literal-block">
<span class="n">source</span> <span class="o">/</span><span class="n">opt</span><span class="o">/</span><span class="n">intel</span><span class="o">/</span><span class="n">parallel_studio_xe_2016</span><span class="o">.</span><span class="mf">3.067</span><span class="o">/</span><span class="n">psxevars</span><span class="o">.</span><span class="n">sh</span> make yes-user-intel
<span class="c1"># or psxevars.csh for C-shell</span> source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh
<span class="n">make</span> <span class="n">intel_cpu_intelmpi</span> # or psxevars.csh for C-shell
</pre></div> make intel_cpu_intelmpi
</div> </pre>
<p>Alternatively, the build can be accomplished with the src/Make.py <p>Alternatively, the build can be accomplished with the src/Make.py
script, described in <a class="reference internal" href="Section_start.html#start-4"><span class="std std-ref">Section 2.4</span></a> of the script, described in <a class="reference internal" href="Section_start.html#start-4"><span class="std std-ref">Section 2.4</span></a> of the
manual. Type &#8220;Make.py -h&#8221; for help. For an example:</p> manual. Type &#8220;Make.py -h&#8221; for help. For an example:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">v</span> <span class="o">-</span><span class="n">p</span> <span class="n">intel</span> <span class="n">omp</span> <span class="o">-</span><span class="n">intel</span> <span class="n">cpu</span> <span class="o">-</span><span class="n">a</span> <span class="n">file</span> <span class="n">intel_cpu_intelmpi</span> <pre class="literal-block">
</pre></div> Make.py -v -p intel omp -intel cpu -a file intel_cpu_intelmpi
</div> </pre>
<p>Note that if you build with support for a Phi coprocessor, the same <p>Note that if you build with support for a Phi coprocessor, the same
binary can be used on nodes with or without coprocessors installed. binary can be used on nodes with or without coprocessors installed.
However, if you do not have coprocessors on your system, building However, if you do not have coprocessors on your system, building
@ -385,10 +385,10 @@ set the number of OpenMP threads via the OMP_NUM_THREADS environment
variable if desired.</p> variable if desired.</p>
<p>Examples (see documentation for your MPI/Machine for differences in <p>Examples (see documentation for your MPI/Machine for differences in
launching MPI applications):</p> launching MPI applications):</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">72</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">36</span> <span class="n">lmp_machine</span> <span class="o">-</span><span class="n">sf</span> <span class="n">intel</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="c1"># 2 nodes, 36 MPI tasks/node, $OMP_NUM_THREADS OpenMP Threads</span> <pre class="literal-block">
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">72</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">36</span> <span class="n">lmp_machine</span> <span class="o">-</span><span class="n">sf</span> <span class="n">intel</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="o">-</span><span class="n">pk</span> <span class="n">intel</span> <span class="mi">0</span> <span class="n">omp</span> <span class="mi">2</span> <span class="n">mode</span> <span class="n">double</span> <span class="c1"># Don&#39;t use any coprocessors that might be available, use 2 OpenMP threads for each task, use double precision</span> mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script # 2 nodes, 36 MPI tasks/node, $OMP_NUM_THREADS OpenMP Threads
</pre></div> mpirun -np 72 -ppn 36 lmp_machine -sf intel -in in.script -pk intel 0 omp 2 mode double # Don't use any coprocessors that might be available, use 2 OpenMP threads for each task, use double precision
</div> </pre>
<p><strong>Or run with the USER-INTEL package by editing an input script:</strong></p> <p><strong>Or run with the USER-INTEL package by editing an input script:</strong></p>
<p>As an alternative to adding command-line arguments, the input script <p>As an alternative to adding command-line arguments, the input script
can be edited to enable the USER-INTEL package. This requires adding can be edited to enable the USER-INTEL package. This requires adding
@ -399,9 +399,9 @@ script. For the second example above, this would be:</p>
</div> </div>
<p>To enable the USER-INTEL package only for individual styles, you can <p>To enable the USER-INTEL package only for individual styles, you can
add an &#8220;intel&#8221; suffix to the individual style, e.g.:</p> add an &#8220;intel&#8221; suffix to the individual style, e.g.:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">intel</span> <span class="mf">2.5</span> <pre class="literal-block">
</pre></div> pair_style lj/cut/intel 2.5
</div> </pre>
<p>Alternatively, the <a class="reference internal" href="suffix.html"><span class="doc">suffix intel</span></a> command can be added to <p>Alternatively, the <a class="reference internal" href="suffix.html"><span class="doc">suffix intel</span></a> command can be added to
the input script to enable USER-INTEL styles for the commands that the input script to enable USER-INTEL styles for the commands that
follow in the input script.</p> follow in the input script.</p>

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@ -166,19 +166,19 @@ produce an executable compatible with specific hardware.</p>
<p>Here is a quick overview of how to use the KOKKOS package <p>Here is a quick overview of how to use the KOKKOS package
for CPU acceleration, assuming one or more 16-core nodes. for CPU acceleration, assuming one or more 16-core nodes.
More details follow.</p> More details follow.</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">use</span> <span class="n">a</span> <span class="n">C</span><span class="o">++</span><span class="mi">11</span> <span class="n">compatible</span> <span class="n">compiler</span> <pre class="literal-block">
<span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">kokkos</span> use a C++11 compatible compiler
<span class="n">make</span> <span class="n">mpi</span> <span class="n">KOKKOS_DEVICES</span><span class="o">=</span><span class="n">OpenMP</span> <span class="c1"># build with the KOKKOS package</span> make yes-kokkos
<span class="n">make</span> <span class="n">kokkos_omp</span> <span class="c1"># or Makefile.kokkos_omp already has variable set</span> make mpi KOKKOS_DEVICES=OpenMP # build with the KOKKOS package
<span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">v</span> <span class="o">-</span><span class="n">p</span> <span class="n">kokkos</span> <span class="o">-</span><span class="n">kokkos</span> <span class="n">omp</span> <span class="o">-</span><span class="n">o</span> <span class="n">mpi</span> <span class="o">-</span><span class="n">a</span> <span class="n">file</span> <span class="n">mpi</span> <span class="c1"># or one-line build via Make.py</span> make kokkos_omp # or Makefile.kokkos_omp already has variable set
</pre></div> Make.py -v -p kokkos -kokkos omp -o mpi -a file mpi # or one-line build via Make.py
</div> </pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">16</span> <span class="n">lmp_mpi</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <span class="c1"># 1 node, 16 MPI tasks/node, no threads</span> <pre class="literal-block">
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">2</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">1</span> <span class="n">lmp_mpi</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">16</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <span class="c1"># 2 nodes, 1 MPI task/node, 16 threads/task</span> mpirun -np 16 lmp_mpi -k on -sf kk -in in.lj # 1 node, 16 MPI tasks/node, no threads
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">2</span> <span class="n">lmp_mpi</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">8</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <span class="c1"># 1 node, 2 MPI tasks/node, 8 threads/task</span> mpirun -np 2 -ppn 1 lmp_mpi -k on t 16 -sf kk -in in.lj # 2 nodes, 1 MPI task/node, 16 threads/task
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">32</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">4</span> <span class="n">lmp_mpi</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">4</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <span class="c1"># 8 nodes, 4 MPI tasks/node, 4 threads/task</span> mpirun -np 2 lmp_mpi -k on t 8 -sf kk -in in.lj # 1 node, 2 MPI tasks/node, 8 threads/task
</pre></div> mpirun -np 32 -ppn 4 lmp_mpi -k on t 4 -sf kk -in in.lj # 8 nodes, 4 MPI tasks/node, 4 threads/task
</div> </pre>
<ul class="simple"> <ul class="simple">
<li>specify variables and settings in your Makefile.machine that enable OpenMP, GPU, or Phi support</li> <li>specify variables and settings in your Makefile.machine that enable OpenMP, GPU, or Phi support</li>
<li>include the KOKKOS package and build LAMMPS</li> <li>include the KOKKOS package and build LAMMPS</li>
@ -188,39 +188,39 @@ More details follow.</p>
assuming one or more nodes, each with 16 cores and a GPU. More assuming one or more nodes, each with 16 cores and a GPU. More
details follow.</p> details follow.</p>
<p>discuss use of NVCC, which Makefiles to examine</p> <p>discuss use of NVCC, which Makefiles to examine</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">use</span> <span class="n">a</span> <span class="n">C</span><span class="o">++</span><span class="mi">11</span> <span class="n">compatible</span> <span class="n">compiler</span> <pre class="literal-block">
<span class="n">KOKKOS_DEVICES</span> <span class="o">=</span> <span class="n">Cuda</span><span class="p">,</span> <span class="n">OpenMP</span> use a C++11 compatible compiler
<span class="n">KOKKOS_ARCH</span> <span class="o">=</span> <span class="n">Kepler35</span> KOKKOS_DEVICES = Cuda, OpenMP
<span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">kokkos</span> KOKKOS_ARCH = Kepler35
<span class="n">make</span> <span class="n">machine</span> make yes-kokkos
<span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="n">kokkos</span> <span class="o">-</span><span class="n">kokkos</span> <span class="n">cuda</span> <span class="n">arch</span><span class="o">=</span><span class="mi">31</span> <span class="o">-</span><span class="n">o</span> <span class="n">kokkos_cuda</span> <span class="o">-</span><span class="n">a</span> <span class="n">file</span> <span class="n">kokkos_cuda</span> make machine
</pre></div> Make.py -p kokkos -kokkos cuda arch=31 -o kokkos_cuda -a file kokkos_cuda
</div> </pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">1</span> <span class="n">lmp_cuda</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">6</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <span class="c1"># one MPI task, 6 threads on CPU</span> <pre class="literal-block">
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">4</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">1</span> <span class="n">lmp_cuda</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">6</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <span class="c1"># ditto on 4 nodes</span> mpirun -np 1 lmp_cuda -k on t 6 -sf kk -in in.lj # one MPI task, 6 threads on CPU
</pre></div> mpirun -np 4 -ppn 1 lmp_cuda -k on t 6 -sf kk -in in.lj # ditto on 4 nodes
</div> </pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">2</span> <span class="n">lmp_cuda</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">8</span> <span class="n">g</span> <span class="mi">2</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <span class="c1"># two MPI tasks, 8 threads per CPU</span> <pre class="literal-block">
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">32</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">2</span> <span class="n">lmp_cuda</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">8</span> <span class="n">g</span> <span class="mi">2</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <span class="c1"># ditto on 16 nodes</span> mpirun -np 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj # two MPI tasks, 8 threads per CPU
</pre></div> mpirun -np 32 -ppn 2 lmp_cuda -k on t 8 g 2 -sf kk -in in.lj # ditto on 16 nodes
</div> </pre>
<p>Here is a quick overview of how to use the KOKKOS package <p>Here is a quick overview of how to use the KOKKOS package
for the Intel Phi:</p> for the Intel Phi:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">use</span> <span class="n">a</span> <span class="n">C</span><span class="o">++</span><span class="mi">11</span> <span class="n">compatible</span> <span class="n">compiler</span> <pre class="literal-block">
<span class="n">KOKKOS_DEVICES</span> <span class="o">=</span> <span class="n">OpenMP</span> use a C++11 compatible compiler
<span class="n">KOKKOS_ARCH</span> <span class="o">=</span> <span class="n">KNC</span> KOKKOS_DEVICES = OpenMP
<span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">kokkos</span> KOKKOS_ARCH = KNC
<span class="n">make</span> <span class="n">machine</span> make yes-kokkos
<span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">p</span> <span class="n">kokkos</span> <span class="o">-</span><span class="n">kokkos</span> <span class="n">phi</span> <span class="o">-</span><span class="n">o</span> <span class="n">kokkos_phi</span> <span class="o">-</span><span class="n">a</span> <span class="n">file</span> <span class="n">mpi</span> make machine
</pre></div> Make.py -p kokkos -kokkos phi -o kokkos_phi -a file mpi
</div> </pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">host</span><span class="o">=</span><span class="n">MIC</span><span class="p">,</span> <span class="n">Intel</span> <span class="n">Phi</span> <span class="k">with</span> <span class="mi">61</span> <span class="n">cores</span> <span class="p">(</span><span class="mi">240</span> <span class="n">threads</span><span class="o">/</span><span class="n">phi</span> <span class="n">via</span> <span class="mi">4</span><span class="n">x</span> <span class="n">hardware</span> <span class="n">threading</span><span class="p">):</span> <pre class="literal-block">
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">1</span> <span class="n">lmp_g</span><span class="o">++</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">240</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <span class="c1"># 1 MPI task on 1 Phi, 1*240 = 240</span> host=MIC, Intel Phi with 61 cores (240 threads/phi via 4x hardware threading):
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">30</span> <span class="n">lmp_g</span><span class="o">++</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">8</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <span class="c1"># 30 MPI tasks on 1 Phi, 30*8 = 240</span> mpirun -np 1 lmp_g++ -k on t 240 -sf kk -in in.lj # 1 MPI task on 1 Phi, 1*240 = 240
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">12</span> <span class="n">lmp_g</span><span class="o">++</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">20</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <span class="c1"># 12 MPI tasks on 1 Phi, 12*20 = 240</span> mpirun -np 30 lmp_g++ -k on t 8 -sf kk -in in.lj # 30 MPI tasks on 1 Phi, 30*8 = 240
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">96</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">12</span> <span class="n">lmp_g</span><span class="o">++</span> <span class="o">-</span><span class="n">k</span> <span class="n">on</span> <span class="n">t</span> <span class="mi">20</span> <span class="o">-</span><span class="n">sf</span> <span class="n">kk</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">lj</span> <span class="c1"># ditto on 8 Phis</span> mpirun -np 12 lmp_g++ -k on t 20 -sf kk -in in.lj # 12 MPI tasks on 1 Phi, 12*20 = 240
</pre></div> mpirun -np 96 -ppn 12 lmp_g++ -k on t 20 -sf kk -in in.lj # ditto on 8 Phis
</div> </pre>
<p><strong>Required hardware/software:</strong></p> <p><strong>Required hardware/software:</strong></p>
<p>Kokkos support within LAMMPS must be built with a C++11 compatible <p>Kokkos support within LAMMPS must be built with a C++11 compatible
compiler. If using gcc, version 4.8.1 or later is required.</p> compiler. If using gcc, version 4.8.1 or later is required.</p>
@ -257,40 +257,40 @@ respectively. Or the effect of the &#8220;-pk&#8221; or &#8220;-sf&#8221; switc
duplicated by adding the <a class="reference internal" href="package.html"><span class="doc">package kokkos</span></a> or <a class="reference internal" href="suffix.html"><span class="doc">suffix kk</span></a> commands respectively to your input script.</p> duplicated by adding the <a class="reference internal" href="package.html"><span class="doc">package kokkos</span></a> or <a class="reference internal" href="suffix.html"><span class="doc">suffix kk</span></a> commands respectively to your input script.</p>
<p>Or you can follow these steps:</p> <p>Or you can follow these steps:</p>
<p>CPU-only (run all-MPI or with OpenMP threading):</p> <p>CPU-only (run all-MPI or with OpenMP threading):</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">cd</span> <span class="n">lammps</span><span class="o">/</span><span class="n">src</span> <pre class="literal-block">
<span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">kokkos</span> cd lammps/src
<span class="n">make</span> <span class="n">g</span><span class="o">++</span> <span class="n">KOKKOS_DEVICES</span><span class="o">=</span><span class="n">OpenMP</span> make yes-kokkos
</pre></div> make g++ KOKKOS_DEVICES=OpenMP
</div> </pre>
<p>Intel Xeon Phi:</p> <p>Intel Xeon Phi:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">cd</span> <span class="n">lammps</span><span class="o">/</span><span class="n">src</span> <pre class="literal-block">
<span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">kokkos</span> cd lammps/src
<span class="n">make</span> <span class="n">g</span><span class="o">++</span> <span class="n">KOKKOS_DEVICES</span><span class="o">=</span><span class="n">OpenMP</span> <span class="n">KOKKOS_ARCH</span><span class="o">=</span><span class="n">KNC</span> make yes-kokkos
</pre></div> make g++ KOKKOS_DEVICES=OpenMP KOKKOS_ARCH=KNC
</div> </pre>
<p>CPUs and GPUs:</p> <p>CPUs and GPUs:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">cd</span> <span class="n">lammps</span><span class="o">/</span><span class="n">src</span> <pre class="literal-block">
<span class="n">make</span> <span class="n">yes</span><span class="o">-</span><span class="n">kokkos</span> cd lammps/src
<span class="n">make</span> <span class="n">cuda</span> <span class="n">KOKKOS_DEVICES</span><span class="o">=</span><span class="n">Cuda</span> make yes-kokkos
</pre></div> make cuda KOKKOS_DEVICES=Cuda
</div> </pre>
<p>These examples set the KOKKOS-specific OMP, MIC, CUDA variables on the <p>These examples set the KOKKOS-specific OMP, MIC, CUDA variables on the
make command line which requires a GNU-compatible make command. Try make command line which requires a GNU-compatible make command. Try
&#8220;gmake&#8221; if your system&#8217;s standard make complains.</p> &#8220;gmake&#8221; if your system&#8217;s standard make complains.</p>
<div class="admonition note"> <div class="admonition note">
<p class="first admonition-title">Note</p> <p class="first admonition-title">Note</p>
<p class="last">If you build using make line variables and re-build LAMMPS twice <p class="last">If you build using make line variables and re-build LAMMPS twice
with different KOKKOS options and the <em>same</em> target, e.g. g++ in the with different KOKKOS options and the *same* target, e.g. g++ in the
first two examples above, then you <em>must</em> perform a &#8220;make clean-all&#8221; first two examples above, then you *must* perform a &#8220;make clean-all&#8221;
or &#8220;make clean-machine&#8221; before each build. This is to force all the or &#8220;make clean-machine&#8221; before each build. This is to force all the
KOKKOS-dependent files to be re-compiled with the new options.</p> KOKKOS-dependent files to be re-compiled with the new options.</p>
</div> </div>
<p>You can also hardwire these make variables in the specified machine <p>You can also hardwire these make variables in the specified machine
makefile, e.g. src/MAKE/Makefile.g++ in the first two examples above, makefile, e.g. src/MAKE/Makefile.g++ in the first two examples above,
with a line like:</p> with a line like:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">KOKKOS_ARCH</span> <span class="o">=</span> <span class="n">KNC</span> <pre class="literal-block">
</pre></div> KOKKOS_ARCH = KNC
</div> </pre>
<p>Note that if you build LAMMPS multiple times in this manner, using <p>Note that if you build LAMMPS multiple times in this manner, using
different KOKKOS options (defined in different machine makefiles), you different KOKKOS options (defined in different machine makefiles), you
do not have to worry about doing a &#8220;clean&#8221; in between. This is do not have to worry about doing a &#8220;clean&#8221; in between. This is
@ -342,7 +342,7 @@ with compute capability 3.x. For the LINK setting, &#8220;nvcc&#8221; should no
be used; instead use g++ or another compiler suitable for linking C++ be used; instead use g++ or another compiler suitable for linking C++
applications. Often you will want to use your MPI compiler wrapper applications. Often you will want to use your MPI compiler wrapper
for this setting (i.e. mpicxx). Finally, the lo-level Makefile must for this setting (i.e. mpicxx). Finally, the lo-level Makefile must
also have a &#8220;Compilation rule&#8221; for creating <a href="#id1"><span class="problematic" id="id2">*</span></a>.o files from <a href="#id3"><span class="problematic" id="id4">*</span></a>.cu files. also have a &#8220;Compilation rule&#8221; for creating *.o files from *.cu files.
See src/Makefile.cuda for an example of a lo-level Makefile with all See src/Makefile.cuda for an example of a lo-level Makefile with all
of these settings.</p> of these settings.</p>
<p>KOKKOS_USE_TPLS=hwloc binds threads to hardware cores, so they do not <p>KOKKOS_USE_TPLS=hwloc binds threads to hardware cores, so they do not
@ -430,9 +430,9 @@ specify its additional arguments for hardware options appopriate to
your system, as documented above.</p> your system, as documented above.</p>
<p>Use the <a class="reference internal" href="suffix.html"><span class="doc">suffix kk</span></a> command, or you can explicitly add a <p>Use the <a class="reference internal" href="suffix.html"><span class="doc">suffix kk</span></a> command, or you can explicitly add a
&#8220;kk&#8221; suffix to individual styles in your input script, e.g.</p> &#8220;kk&#8221; suffix to individual styles in your input script, e.g.</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">kk</span> <span class="mf">2.5</span> <pre class="literal-block">
</pre></div> pair_style lj/cut/kk 2.5
</div> </pre>
<p>You only need to use the <a class="reference internal" href="package.html"><span class="doc">package kokkos</span></a> command if you <p>You only need to use the <a class="reference internal" href="package.html"><span class="doc">package kokkos</span></a> command if you
wish to change any of its option defaults, as set by the &#8220;-k on&#8221; wish to change any of its option defaults, as set by the &#8220;-k on&#8221;
<a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a>.</p> <a class="reference internal" href="Section_start.html#start-7"><span class="std std-ref">command-line switch</span></a>.</p>
@ -483,10 +483,10 @@ performance to bind both MPI tasks to physical cores, and threads to
physical cores, so they do not migrate during a simulation.</p> physical cores, so they do not migrate during a simulation.</p>
<p>If you are not certain MPI tasks are being bound (check the defaults <p>If you are not certain MPI tasks are being bound (check the defaults
for your MPI installation), binding can be forced with these flags:</p> for your MPI installation), binding can be forced with these flags:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">OpenMPI</span> <span class="mf">1.8</span><span class="p">:</span> <span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">2</span> <span class="o">-</span><span class="n">bind</span><span class="o">-</span><span class="n">to</span> <span class="n">socket</span> <span class="o">-</span><span class="nb">map</span><span class="o">-</span><span class="n">by</span> <span class="n">socket</span> <span class="o">./</span><span class="n">lmp_openmpi</span> <span class="o">...</span> <pre class="literal-block">
<span class="n">Mvapich2</span> <span class="mf">2.0</span><span class="p">:</span> <span class="n">mpiexec</span> <span class="o">-</span><span class="n">np</span> <span class="mi">2</span> <span class="o">-</span><span class="n">bind</span><span class="o">-</span><span class="n">to</span> <span class="n">socket</span> <span class="o">-</span><span class="nb">map</span><span class="o">-</span><span class="n">by</span> <span class="n">socket</span> <span class="o">./</span><span class="n">lmp_mvapich</span> <span class="o">...</span> OpenMPI 1.8: mpirun -np 2 -bind-to socket -map-by socket ./lmp_openmpi ...
</pre></div> Mvapich2 2.0: mpiexec -np 2 -bind-to socket -map-by socket ./lmp_mvapich ...
</div> </pre>
<p>For binding threads with the KOKKOS OMP option, use thread affinity <p>For binding threads with the KOKKOS OMP option, use thread affinity
environment variables to force binding. With OpenMP 3.1 (gcc 4.7 or environment variables to force binding. With OpenMP 3.1 (gcc 4.7 or
later, intel 12 or later) setting the environment variable later, intel 12 or later) setting the environment variable

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@ -141,11 +141,11 @@ one or more 16-core nodes. More details follow.</p>
<span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">v</span> <span class="o">-</span><span class="n">p</span> <span class="n">omp</span> <span class="o">-</span><span class="n">o</span> <span class="n">mpi</span> <span class="o">-</span><span class="n">a</span> <span class="n">file</span> <span class="n">mpi</span> <span class="c1"># or one-line build via Make.py</span> <span class="n">Make</span><span class="o">.</span><span class="n">py</span> <span class="o">-</span><span class="n">v</span> <span class="o">-</span><span class="n">p</span> <span class="n">omp</span> <span class="o">-</span><span class="n">o</span> <span class="n">mpi</span> <span class="o">-</span><span class="n">a</span> <span class="n">file</span> <span class="n">mpi</span> <span class="c1"># or one-line build via Make.py</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">lmp_mpi</span> <span class="o">-</span><span class="n">sf</span> <span class="n">omp</span> <span class="o">-</span><span class="n">pk</span> <span class="n">omp</span> <span class="mi">16</span> <span class="o">&lt;</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="c1"># 1 MPI task, 16 threads</span> <pre class="literal-block">
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">4</span> <span class="n">lmp_mpi</span> <span class="o">-</span><span class="n">sf</span> <span class="n">omp</span> <span class="o">-</span><span class="n">pk</span> <span class="n">omp</span> <span class="mi">4</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="c1"># 4 MPI tasks, 4 threads/task</span> lmp_mpi -sf omp -pk omp 16 &lt; in.script # 1 MPI task, 16 threads
<span class="n">mpirun</span> <span class="o">-</span><span class="n">np</span> <span class="mi">32</span> <span class="o">-</span><span class="n">ppn</span> <span class="mi">4</span> <span class="n">lmp_mpi</span> <span class="o">-</span><span class="n">sf</span> <span class="n">omp</span> <span class="o">-</span><span class="n">pk</span> <span class="n">omp</span> <span class="mi">4</span> <span class="o">-</span><span class="ow">in</span> <span class="ow">in</span><span class="o">.</span><span class="n">script</span> <span class="c1"># 8 nodes, 4 MPI tasks/node, 4 threads/task</span> mpirun -np 4 lmp_mpi -sf omp -pk omp 4 -in in.script # 4 MPI tasks, 4 threads/task
</pre></div> mpirun -np 32 -ppn 4 lmp_mpi -sf omp -pk omp 4 -in in.script # 8 nodes, 4 MPI tasks/node, 4 threads/task
</div> </pre>
<p><strong>Required hardware/software:</strong></p> <p><strong>Required hardware/software:</strong></p>
<p>Your compiler must support the OpenMP interface. You should have one <p>Your compiler must support the OpenMP interface. You should have one
or more multi-core CPUs so that multiple threads can be launched by or more multi-core CPUs so that multiple threads can be launched by
@ -184,9 +184,9 @@ threads via the OMP_NUM_THREADS environment variable.</p>
and threads/MPI task is the same.</p> and threads/MPI task is the same.</p>
<p>Use the <a class="reference internal" href="suffix.html"><span class="doc">suffix omp</span></a> command, or you can explicitly add an <p>Use the <a class="reference internal" href="suffix.html"><span class="doc">suffix omp</span></a> command, or you can explicitly add an
&#8220;omp&#8221; suffix to individual styles in your input script, e.g.</p> &#8220;omp&#8221; suffix to individual styles in your input script, e.g.</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span><span class="o">/</span><span class="n">omp</span> <span class="mf">2.5</span> <pre class="literal-block">
</pre></div> pair_style lj/cut/omp 2.5
</div> </pre>
<p>You must also use the <a class="reference internal" href="package.html"><span class="doc">package omp</span></a> command to enable the <p>You must also use the <a class="reference internal" href="package.html"><span class="doc">package omp</span></a> command to enable the
USER-OMP package. When you do this you also specify how many threads USER-OMP package. When you do this you also specify how many threads
per MPI task to use. The command doc page explains other options and per MPI task to use. The command doc page explains other options and

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@ -137,16 +137,16 @@
<h1>angle_style charmm/omp command</h1> <h1>angle_style charmm/omp command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">charmm</span> <pre class="literal-block">
</pre></div> angle_style charmm
</div> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">charmm</span> <pre class="literal-block">
<span class="n">angle_coeff</span> <span class="mi">1</span> <span class="mf">300.0</span> <span class="mf">107.0</span> <span class="mf">50.0</span> <span class="mf">3.0</span> angle_style charmm
</pre></div> angle_coeff 1 300.0 107.0 50.0 3.0
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>

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@ -131,18 +131,18 @@
<h1>angle_style class2/omp command</h1> <h1>angle_style class2/omp command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">class2</span> <pre class="literal-block">
</pre></div> angle_style class2
</div> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">class2</span> <pre class="literal-block">
<span class="n">angle_coeff</span> <span class="o">*</span> <span class="mf">75.0</span> angle_style class2
<span class="n">angle_coeff</span> <span class="mi">1</span> <span class="n">bb</span> <span class="mf">10.5872</span> <span class="mf">1.0119</span> <span class="mf">1.5228</span> angle_coeff * 75.0
<span class="n">angle_coeff</span> <span class="o">*</span> <span class="n">ba</span> <span class="mf">3.6551</span> <span class="mf">24.895</span> <span class="mf">1.0119</span> <span class="mf">1.5228</span> angle_coeff 1 bb 10.5872 1.0119 1.5228
</pre></div> angle_coeff * ba 3.6551 24.895 1.0119 1.5228
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>

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@ -131,16 +131,16 @@
<h1>angle_style cosine/omp command</h1> <h1>angle_style cosine/omp command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span> <pre class="literal-block">
</pre></div> angle_style cosine
</div> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span> <pre class="literal-block">
<span class="n">angle_coeff</span> <span class="o">*</span> <span class="mf">75.0</span> angle_style cosine
</pre></div> angle_coeff * 75.0
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>

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@ -131,16 +131,16 @@
<h1>angle_style cosine/delta/omp command</h1> <h1>angle_style cosine/delta/omp command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">delta</span> <pre class="literal-block">
</pre></div> angle_style cosine/delta
</div> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">delta</span> <pre class="literal-block">
<span class="n">angle_coeff</span> <span class="mi">2</span><span class="o">*</span><span class="mi">4</span> <span class="mf">75.0</span> <span class="mf">100.0</span> angle_style cosine/delta
</pre></div> angle_coeff 2*4 75.0 100.0
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>

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@ -131,16 +131,16 @@
<h1>angle_style cosine/periodic/omp command</h1> <h1>angle_style cosine/periodic/omp command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">periodic</span> <pre class="literal-block">
</pre></div> angle_style cosine/periodic
</div> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">periodic</span> <pre class="literal-block">
<span class="n">angle_coeff</span> <span class="o">*</span> <span class="mf">75.0</span> <span class="mi">1</span> <span class="mi">6</span> angle_style cosine/periodic
</pre></div> angle_coeff * 75.0 1 6
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>

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@ -131,16 +131,16 @@
<h1>angle_style cosine/shift/omp command</h1> <h1>angle_style cosine/shift/omp command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">shift</span> <pre class="literal-block">
</pre></div> angle_style cosine/shift
</div> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">shift</span> <pre class="literal-block">
<span class="n">angle_coeff</span> <span class="o">*</span> <span class="mf">10.0</span> <span class="mf">45.0</span> angle_style cosine/shift
</pre></div> angle_coeff * 10.0 45.0
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>

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@ -131,16 +131,16 @@
<h1>angle_style cosine/shift/exp/omp command</h1> <h1>angle_style cosine/shift/exp/omp command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">shift</span><span class="o">/</span><span class="n">exp</span> <pre class="literal-block">
</pre></div> angle_style cosine/shift/exp
</div> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">shift</span><span class="o">/</span><span class="n">exp</span> <pre class="literal-block">
<span class="n">angle_coeff</span> <span class="o">*</span> <span class="mf">10.0</span> <span class="mf">45.0</span> <span class="mf">2.0</span> angle_style cosine/shift/exp
</pre></div> angle_coeff * 10.0 45.0 2.0
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>

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@ -131,16 +131,16 @@
<h1>angle_style cosine/squared/omp command</h1> <h1>angle_style cosine/squared/omp command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">squared</span> <pre class="literal-block">
</pre></div> angle_style cosine/squared
</div> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">squared</span> <pre class="literal-block">
<span class="n">angle_coeff</span> <span class="mi">2</span><span class="o">*</span><span class="mi">4</span> <span class="mf">75.0</span> <span class="mf">100.0</span> angle_style cosine/squared
</pre></div> angle_coeff 2*4 75.0 100.0
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>

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@ -131,16 +131,16 @@
<h1>angle_style dipole/omp command</h1> <h1>angle_style dipole/omp command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">dipole</span> <pre class="literal-block">
</pre></div> angle_style dipole
</div> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">dipole</span> <pre class="literal-block">
<span class="n">angle_coeff</span> <span class="mi">6</span> <span class="mf">2.1</span> <span class="mf">180.0</span> angle_style dipole
</pre></div> angle_coeff 6 2.1 180.0
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>

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@ -131,9 +131,9 @@
<h1>angle_style fourier/omp command</h1> <h1>angle_style fourier/omp command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">fourier</span> <pre class="literal-block">
</pre></div> angle_style fourier
</div> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>

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@ -131,9 +131,9 @@
<h1>angle_style fourier/simple/omp command</h1> <h1>angle_style fourier/simple/omp command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">fourier</span><span class="o">/</span><span class="n">simple</span> <pre class="literal-block">
</pre></div> angle_style fourier/simple
</div> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>

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@ -137,16 +137,16 @@
<h1>angle_style harmonic/omp command</h1> <h1>angle_style harmonic/omp command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">harmonic</span> <pre class="literal-block">
</pre></div> angle_style harmonic
</div> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">harmonic</span> <pre class="literal-block">
<span class="n">angle_coeff</span> <span class="mi">1</span> <span class="mf">300.0</span> <span class="mf">107.0</span> angle_style harmonic
</pre></div> angle_coeff 1 300.0 107.0
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>

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@ -131,16 +131,16 @@
<h1>angle_style quartic/omp command</h1> <h1>angle_style quartic/omp command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">quartic</span> <pre class="literal-block">
</pre></div> angle_style quartic
</div> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">quartic</span> <pre class="literal-block">
<span class="n">angle_coeff</span> <span class="mi">1</span> <span class="mf">129.1948</span> <span class="mf">56.8726</span> <span class="o">-</span><span class="mf">25.9442</span> <span class="o">-</span><span class="mf">14.2221</span> angle_style quartic
</pre></div> angle_coeff 1 129.1948 56.8726 -25.9442 -14.2221
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>

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@ -128,19 +128,19 @@
<span id="index-0"></span><h1>angle_style sdk command</h1> <span id="index-0"></span><h1>angle_style sdk command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">sdk</span> <pre class="literal-block">
</pre></div> angle_style sdk
</div> </pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">sdk</span><span class="o">/</span><span class="n">omp</span> <pre class="literal-block">
</pre></div> angle_style sdk/omp
</div> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">angle_style</span> <span class="n">sdk</span> <pre class="literal-block">
<span class="n">angle_coeff</span> <span class="mi">1</span> <span class="mf">300.0</span> <span class="mf">107.0</span> angle_style sdk
</pre></div> angle_coeff 1 300.0 107.0
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>

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

24
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@ -128,9 +128,9 @@
<span id="index-0"></span><h1>atom_style command</h1> <span id="index-0"></span><h1>atom_style command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<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 class="literal-block">
</pre></div> atom_style style args
</div> </pre>
<ul class="simple"> <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> <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> </ul>
@ -150,15 +150,15 @@ args = none for any style except the following
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">atom_style</span> <span class="n">atomic</span> <pre class="literal-block">
<span class="n">atom_style</span> <span class="n">bond</span> atom_style atomic
<span class="n">atom_style</span> <span class="n">full</span> atom_style bond
<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> atom_style full
<span class="n">atom_style</span> <span class="n">hybrid</span> <span class="n">charge</span> <span class="n">bond</span> atom_style body nparticle 2 10
<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> atom_style hybrid charge bond
<span class="n">atom_style</span> <span class="n">template</span> <span class="n">myMols</span> atom_style hybrid charge body nparticle 2 5
</pre></div> atom_style template myMols
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>

20
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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> duplicates its functionality.</p>
<p>The atom_style body command for this body style takes two additional <p>The atom_style body command for this body style takes two additional
arguments:</p> arguments:</p>
<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> <pre class="literal-block">
<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> atom_style body nparticle Nmin Nmax
<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> Nmin = minimum # of sub-particles in any body in the system
</pre></div> Nmax = maximum # of sub-particles in any body in the system
</div> </pre>
<p>The Nmin and Nmax arguments are used to bound the size of data <p>The Nmin and Nmax arguments are used to bound the size of data
structures used internally by each particle.</p> 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 <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 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 body style <em>nparticle</em>, the atom_style body command for this body
style takes two additional arguments:</p> style takes two additional arguments:</p>
<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> <pre class="literal-block">
<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> atom_style body rounded/polygon Nmin Nmax
<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> Nmin = minimum # of vertices in any body in the system
</pre></div> Nmax = maximum # of vertices in any body in the system
</div> </pre>
<p>The Nmin and Nmax arguments are used to bound the size of data <p>The Nmin and Nmax arguments are used to bound the size of data
structures used internally by each particle.</p> 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 <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

14
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@ -131,16 +131,16 @@
<h1>bond_style class2/omp command</h1> <h1>bond_style class2/omp command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">class2</span> <pre class="literal-block">
</pre></div> bond_style class2
</div> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">class2</span> <pre class="literal-block">
<span class="n">bond_coeff</span> <span class="mi">1</span> <span class="mf">1.0</span> <span class="mf">100.0</span> <span class="mf">80.0</span> <span class="mf">80.0</span> bond_style class2
</pre></div> bond_coeff 1 1.0 100.0 80.0 80.0
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>

14
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@ -137,16 +137,16 @@
<h1>bond_style fene/omp command</h1> <h1>bond_style fene/omp command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">fene</span> <pre class="literal-block">
</pre></div> bond_style fene
</div> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">fene</span> <pre class="literal-block">
<span class="n">bond_coeff</span> <span class="mi">1</span> <span class="mf">30.0</span> <span class="mf">1.5</span> <span class="mf">1.0</span> <span class="mf">1.0</span> bond_style fene
</pre></div> bond_coeff 1 30.0 1.5 1.0 1.0
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>

14
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@ -131,16 +131,16 @@
<h1>bond_style fene/expand/omp command</h1> <h1>bond_style fene/expand/omp command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">fene</span><span class="o">/</span><span class="n">expand</span> <pre class="literal-block">
</pre></div> bond_style fene/expand
</div> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">fene</span><span class="o">/</span><span class="n">expand</span> <pre class="literal-block">
<span class="n">bond_coeff</span> <span class="mi">1</span> <span class="mf">30.0</span> <span class="mf">1.5</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">0.5</span> bond_style fene/expand
</pre></div> bond_coeff 1 30.0 1.5 1.0 1.0 0.5
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>

14
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@ -137,16 +137,16 @@
<h1>bond_style harmonic/omp command</h1> <h1>bond_style harmonic/omp command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</span> <pre class="literal-block">
</pre></div> bond_style harmonic
</div> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</span> <pre class="literal-block">
<span class="n">bond_coeff</span> <span class="mi">5</span> <span class="mf">80.0</span> <span class="mf">1.2</span> bond_style harmonic
</pre></div> bond_coeff 5 80.0 1.2
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>

14
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@ -131,16 +131,16 @@
<h1>bond_style harmonic/shift/omp command</h1> <h1>bond_style harmonic/shift/omp command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</span><span class="o">/</span><span class="n">shift</span> <pre class="literal-block">
</pre></div> bond_style harmonic/shift
</div> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</span><span class="o">/</span><span class="n">shift</span> <pre class="literal-block">
<span class="n">bond_coeff</span> <span class="mi">5</span> <span class="mf">10.0</span> <span class="mf">0.5</span> <span class="mf">1.0</span> bond_style harmonic/shift
</pre></div> bond_coeff 5 10.0 0.5 1.0
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>

14
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@ -131,16 +131,16 @@
<h1>bond_style harmonic/shift/cut/omp command</h1> <h1>bond_style harmonic/shift/cut/omp command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</span><span class="o">/</span><span class="n">shift</span><span class="o">/</span><span class="n">cut</span> <pre class="literal-block">
</pre></div> bond_style harmonic/shift/cut
</div> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">harmonic</span><span class="o">/</span><span class="n">shift</span><span class="o">/</span><span class="n">cut</span> <pre class="literal-block">
<span class="n">bond_coeff</span> <span class="mi">5</span> <span class="mf">10.0</span> <span class="mf">0.5</span> <span class="mf">1.0</span> bond_style harmonic/shift/cut
</pre></div> bond_coeff 5 10.0 0.5 1.0
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>

14
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@ -131,16 +131,16 @@
<h1>bond_style morse/omp command</h1> <h1>bond_style morse/omp command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">morse</span> <pre class="literal-block">
</pre></div> bond_style morse
</div> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">morse</span> <pre class="literal-block">
<span class="n">bond_coeff</span> <span class="mi">5</span> <span class="mf">1.0</span> <span class="mf">2.0</span> <span class="mf">1.2</span> bond_style morse
</pre></div> bond_coeff 5 1.0 2.0 1.2
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>

14
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@ -131,16 +131,16 @@
<h1>bond_style nonlinear/omp command</h1> <h1>bond_style nonlinear/omp command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">nonlinear</span> <pre class="literal-block">
</pre></div> bond_style nonlinear
</div> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">nonlinear</span> <pre class="literal-block">
<span class="n">bond_coeff</span> <span class="mi">2</span> <span class="mf">100.0</span> <span class="mf">1.1</span> <span class="mf">1.4</span> bond_style nonlinear
</pre></div> bond_coeff 2 100.0 1.1 1.4
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>

22
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@ -131,16 +131,16 @@
<h1>bond_style quartic/omp command</h1> <h1>bond_style quartic/omp command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">quartic</span> <pre class="literal-block">
</pre></div> bond_style quartic
</div> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">bond_style</span> <span class="n">quartic</span> <pre class="literal-block">
<span class="n">bond_coeff</span> <span class="mi">2</span> <span class="mi">1200</span> <span class="o">-</span><span class="mf">0.55</span> <span class="mf">0.25</span> <span class="mf">1.3</span> <span class="mf">34.6878</span> bond_style quartic
</pre></div> bond_coeff 2 1200 -0.55 0.25 1.3 34.6878
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>
@ -184,10 +184,10 @@ to 1,1,1, as indicated as a restriction below.</p>
<p>Note that when bonds are dumped to a file via the <a class="reference internal" href="dump.html"><span class="doc">dump local</span></a> command, bonds with type 0 are not included. The <p>Note that when bonds are dumped to a file via the <a class="reference internal" href="dump.html"><span class="doc">dump local</span></a> command, bonds with type 0 are not included. The
<a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></a> command can also be used to query the <a class="reference internal" href="delete_bonds.html"><span class="doc">delete_bonds</span></a> command can also be used to query the
status of broken bonds or permanently delete them, e.g.:</p> status of broken bonds or permanently delete them, e.g.:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">delete_bonds</span> <span class="nb">all</span> <span class="n">stats</span> <pre class="literal-block">
<span class="n">delete_bonds</span> <span class="nb">all</span> <span class="n">bond</span> <span class="mi">0</span> <span class="n">remove</span> delete_bonds all stats
</pre></div> delete_bonds all bond 0 remove
</div> </pre>
<hr class="docutils" /> <hr class="docutils" />
<p>Styles with a <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are <p>Styles with a <em>gpu</em>, <em>intel</em>, <em>kk</em>, <em>omp</em>, or <em>opt</em> suffix are
functionally the same as the corresponding style without the suffix. functionally the same as the corresponding style without the suffix.

56
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@ -128,9 +128,9 @@
<span id="index-0"></span><h1>change_box command</h1> <span id="index-0"></span><h1>change_box command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<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 class="literal-block">
</pre></div> change_box group-ID parameter args ... keyword args ...
</div> </pre>
<ul class="simple"> <ul class="simple">
<li>group-ID = ID of group of atoms to (optionally) displace</li> <li>group-ID = ID of group of atoms to (optionally) displace</li>
<li>one or more parameter/arg pairs may be appended</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>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<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> <pre class="literal-block">
<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> change_box all xy final -2.0 z final 0.0 5.0 boundary p p f remap units box
</pre></div> change_box all x scale 1.1 y volume z volume remap
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <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 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> is non-periodic and atoms extend from 0 to 20 in all dimensions:</p>
</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> <pre class="literal-block">
<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> change_box all x final -10 20
</pre></div> create_atoms 1 single -5 5 5 # this will fail to insert an atom
</div> </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">boundary</span> <span class="n">f</span> <span class="n">s</span> <span class="n">s</span> <pre class="literal-block">
<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> change_box all x final -10 20 boundary f s s
<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> create_atoms 1 single -5 5 5
</pre></div> change_box boundary s s s # this will work
</div> </pre>
<div class="admonition note"> <div class="admonition note">
<p class="first admonition-title">Note</p> <p class="first admonition-title">Note</p>
<p class="last">Unlike the earlier &#8220;displace_box&#8221; version of this command, atom <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> <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 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> preceding &#8220;key&#8221;. I.e. this sequence of keywords is allowed:</p>
<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 class="literal-block">
</pre></div> change_box all x scale 1.1 y volume z volume
</div> </pre>
<p>The <em>volume</em> style changes the associated dimension so that the <p>The <em>volume</em> style changes the associated dimension so that the
overall box volume is unchanged relative to its value before the overall box volume is unchanged relative to its value before the
preceding keyword was invoked.</p> preceding keyword was invoked.</p>
<p>If the following command is used, then the z box length will shrink by <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> the same 1.1 factor the x box length was increased by:</p>
<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 class="literal-block">
</pre></div> change_box all x scale 1.1 z volume
</div> </pre>
<p>If the following command is used, then the y,z box lengths will each <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 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 y,z box lengths shrink so as to keep their relative aspect ratio
constant:</p> constant:</p>
<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 class="literal-block">
</pre></div> change_box all&quot;x scale 1.1 y volume z volume
</div> </pre>
<p>If the following command is used, then the final box will be a factor <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 of 10% larger in x and y, and a factor of 21% smaller in z, so as to
keep the volume constant:</p> keep the volume constant:</p>
<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 class="literal-block">
</pre></div> change_box all x scale 1.1 z volume y scale 1.1 z volume
</div> </pre>
<div class="admonition note"> <div class="admonition note">
<p class="first admonition-title">Note</p> <p class="first admonition-title">Note</p>
<p class="last">For solids or liquids, when one dimension of the box is <p class="last">For solids or liquids, when one dimension of the box is

14
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@ -186,8 +186,8 @@ discussed below, it can be referenced via the following bracket
notation, where ID is the ID of the compute:</p> notation, where ID is the ID of the compute:</p>
<table border="1" class="docutils"> <table border="1" class="docutils">
<colgroup> <colgroup>
<col width="21%" /> <col width="23%" />
<col width="79%" /> <col width="77%" />
</colgroup> </colgroup>
<tbody valign="top"> <tbody valign="top">
<tr class="row-odd"><td>c_ID</td> <tr class="row-odd"><td>c_ID</td>
@ -245,11 +245,11 @@ computes for further info.</p>
Three computes are always created, named &#8220;thermo_temp&#8221;, Three computes are always created, named &#8220;thermo_temp&#8221;,
&#8220;thermo_press&#8221;, and &#8220;thermo_pe&#8221;, as if these commands had been invoked &#8220;thermo_press&#8221;, and &#8220;thermo_pe&#8221;, as if these commands had been invoked
in the input script:</p> in the input script:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">thermo_temp</span> <span class="nb">all</span> <span class="n">temp</span> <pre class="literal-block">
<span class="n">compute</span> <span class="n">thermo_press</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">thermo_temp</span> compute thermo_temp all temp
<span class="n">compute</span> <span class="n">thermo_pe</span> <span class="nb">all</span> <span class="n">pe</span> compute thermo_press all pressure thermo_temp
</pre></div> compute thermo_pe all pe
</div> </pre>
<p>Additional computes for other quantities are created if the thermo <p>Additional computes for other quantities are created if the thermo
style requires it. See the documentation for the style requires it. See the documentation for the
<a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command.</p> <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command.</p>

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@ -177,11 +177,11 @@ For example, bond output from the <a class="reference internal" href="compute_pr
with data from this command and output by the <a class="reference internal" href="dump.html"><span class="doc">dump local</span></a> with data from this command and output by the <a class="reference internal" href="dump.html"><span class="doc">dump local</span></a>
command in a consistent way.</p> command in a consistent way.</p>
<p>Here is an example of how to do this:</p> <p>Here is an example of how to do this:</p>
<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">btype</span> <span class="n">batom1</span> <span class="n">batom2</span> <pre class="literal-block">
<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> compute 1 all property/local btype batom1 batom2
<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> compute 2 all bond/local dist eng
</pre></div> dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2]
</div> </pre>
<p><strong>Output info:</strong></p> <p><strong>Output info:</strong></p>
<p>This compute calculates a local vector or local array depending on the <p>This compute calculates a local vector or local array depending on the
number of keywords. The length of the vector or number of rows in the number of keywords. The length of the vector or number of rows in the

2
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@ -234,7 +234,7 @@ simulation into gold (FCC). These were provided by Jon Zimmerman
<span class="n">Free</span> <span class="n">surface</span> <span class="o">~</span> <span class="mf">23.0</span> <span class="n">Free</span> <span class="n">surface</span> <span class="o">~</span> <span class="mf">23.0</span>
</pre></div> </pre></div>
</div> </div>
<p>These values are <em>not</em> normalized by the square of the lattice <p>These values are *not* normalized by the square of the lattice
parameter. If they were, normalized values would be:</p> parameter. If they were, normalized values would be:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Bulk</span> <span class="n">lattice</span> <span class="o">=</span> <span class="mi">0</span> <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Bulk</span> <span class="n">lattice</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">Dislocation</span> <span class="n">core</span> <span class="o">~</span> <span class="mf">0.06</span> <span class="p">(</span><span class="mf">0.03</span> <span class="n">to</span> <span class="mf">0.075</span><span class="p">)</span> <span class="n">Dislocation</span> <span class="n">core</span> <span class="o">~</span> <span class="mf">0.06</span> <span class="p">(</span><span class="mf">0.03</span> <span class="n">to</span> <span class="mf">0.075</span><span class="p">)</span>

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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 <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> 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> command, for example:</p>
<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> <pre class="literal-block">
<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> compute cc1 all chunk/atom molecule
<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> compute myChunk all dipole/chunk cc1
</pre></div> fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
</div> </pre>
<p><strong>Output info:</strong></p> <p><strong>Output info:</strong></p>
<p>This compute calculates a global array where the number of rows = the <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 = 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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@ -164,10 +164,10 @@
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<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">fep</span> <span class="mi">298</span> <span class="n">pair</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="n">epsilon</span> <span class="mi">1</span> <span class="o">*</span> <span class="n">v_delta</span> <span class="n">pair</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="n">sigma</span> <span class="mi">1</span> <span class="o">*</span> <span class="n">v_delta</span> <span class="n">volume</span> <span class="n">yes</span> <pre class="literal-block">
<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">fep</span> <span class="mi">300</span> <span class="n">atom</span> <span class="n">charge</span> <span class="mi">2</span> <span class="n">v_delta</span> compute 1 all fep 298 pair lj/cut epsilon 1 * v_delta pair lj/cut sigma 1 * v_delta volume yes
</pre></div> compute 1 all fep 300 atom charge 2 v_delta
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>
@ -307,7 +307,7 @@ each, as in the 1st example above. I &lt;= J is required. LAMMPS sets
the coefficients for the symmetric J,I interaction to the same the coefficients for the symmetric J,I interaction to the same
values. A wild-card asterisk can be used in place of or in conjunction values. A wild-card asterisk can be used in place of or in conjunction
with the I,J arguments to set the coefficients for multiple pairs of with the I,J arguments to set the coefficients for multiple pairs of
atom types. This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or &#8220;m*n&#8221;. If N = 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 an asterisk with no numeric values 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 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 1 to n (inclusive). A trailing asterisk means all types from n to N

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@ -193,11 +193,11 @@ using the <a class="reference internal" href="set.html"><span class="doc">set im
<p>The simplest way to output the results of the compute gyration/chunk <p>The simplest way to output the results of the compute gyration/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> 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> command, for example:</p>
<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> <pre class="literal-block">
<span class="n">compute</span> <span class="n">myChunk</span> <span class="nb">all</span> <span class="n">gyration</span><span class="o">/</span><span class="n">chunk</span> <span class="n">cc1</span> compute cc1 all chunk/atom molecule
<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="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> compute myChunk all gyration/chunk cc1
</pre></div> fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
</div> </pre>
<p><strong>Output info:</strong></p> <p><strong>Output info:</strong></p>
<p>This compute calculates a global vector if the <em>tensor</em> keyword is not <p>This compute calculates a global vector if the <em>tensor</em> keyword is not
specified and a global array if it is. The length of the vector or specified and a global array if it is. The length of the vector or

26
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@ -237,29 +237,30 @@ energy/area/time <a class="reference internal" href="units.html"><span class="do
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Sample LAMMPS input script for thermal conductivity of solid Ar</span> <div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Sample LAMMPS input script for thermal conductivity of solid Ar</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span>units real <pre class="literal-block">
units real
variable T equal 70 variable T equal 70
variable V equal vol variable V equal vol
variable dt equal 4.0 variable dt equal 4.0
variable p equal 200 # correlation length variable p equal 200 # correlation length
variable s equal 10 # sample interval variable s equal 10 # sample interval
variable d equal $p*$s # dump interval variable d equal $p*$s # dump interval
</pre></div> </pre>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># convert from LAMMPS real units to SI</span> <div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># convert from LAMMPS real units to SI</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span>variable kB equal 1.3806504e-23 # [J/K] Boltzmann <pre class="literal-block">
variable kB equal 1.3806504e-23 # [J/K] Boltzmann
variable kCal2J equal 4186.0/6.02214e23 variable kCal2J equal 4186.0/6.02214e23
variable A2m equal 1.0e-10 variable A2m equal 1.0e-10
variable fs2s equal 1.0e-15 variable fs2s equal 1.0e-15
variable convert equal ${kCal2J}*${kCal2J}/${fs2s}/${A2m} variable convert equal ${kCal2J}*${kCal2J}/${fs2s}/${A2m}
</pre></div> </pre>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># setup problem</span> <div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># setup problem</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span>dimension 3 <pre class="literal-block">
dimension 3
boundary p p p boundary p p p
lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1 lattice fcc 5.376 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
region box block 0 4 0 4 0 4 region box block 0 4 0 4 0 4
@ -270,8 +271,7 @@ pair_style lj/cut 13.0
pair_coeff * * 0.2381 3.405 pair_coeff * * 0.2381 3.405
timestep ${dt} timestep ${dt}
thermo $d thermo $d
</pre></div> </pre>
</div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># equilibration and thermalization</span> <div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># equilibration and thermalization</span>
</pre></div> </pre></div>
</div> </div>
@ -287,7 +287,8 @@ run 8000
<span class="c1">#fix NVE all nve</span> <span class="c1">#fix NVE all nve</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span>reset_timestep 0 <pre class="literal-block">
reset_timestep 0
compute myKE all ke/atom compute myKE all ke/atom
compute myPE all pe/atom compute myPE all pe/atom
compute myStress all stress/atom NULL virial compute myStress all stress/atom NULL virial
@ -305,9 +306,8 @@ thermo_style custom step temp v_Jx v_Jy v_Jz v_k11 v_k22 v_k33
run 100000 run 100000
variable k equal (v_k11+v_k22+v_k33)/3.0 variable k equal (v_k11+v_k22+v_k33)/3.0
variable ndens equal count(all)/vol variable ndens equal count(all)/vol
print &quot;average conductivity: $k[W/mK] @ $T K, ${ndens} /A^3&quot; print &quot;average conductivity: $k[W/mK] &#64; $T K, ${ndens} /A^3&quot;
</pre></div> </pre>
</div>
</div> </div>
</div> </div>

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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 <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> 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> command, for example:</p>
<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> <pre class="literal-block">
<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> compute cc1 all chunk/atom molecule
<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> compute myChunk all inertia/chunk cc1
</pre></div> fix 1 all ave/time 100 1 100 c_myChunk[*] file tmp.out mode vector
</div> </pre>
<p><strong>Output info:</strong></p> <p><strong>Output info:</strong></p>
<p>This compute calculates a global array where the number of rows = the <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 = 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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@ -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> 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> command, as shown in the following example:</p>
</div> </div>
<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> <pre class="literal-block">
<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> compute effTemp all temp/eff
<span class="n">thermo_modify</span> <span class="n">temp</span> <span class="n">effTemp</span> thermo_style custom step etotal pe ke temp press
</pre></div> thermo_modify temp effTemp
</div> </pre>
<p>The value of the kinetic energy will be 0.0 for atoms (nuclei or <p>The value of the kinetic energy will be 0.0 for atoms (nuclei or
electrons) not in the specified compute group.</p> electrons) not in the specified compute group.</p>
<p><strong>Output info:</strong></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 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 <a class="reference internal" href="thermo_modify.html"><span class="doc">thermo_modify</span></a> command, as shown in the following
example:</p> example:</p>
<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> <pre class="literal-block">
<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> compute effTemp all temp/eff
<span class="n">thermo_modify</span> <span class="n">temp</span> <span class="n">effTemp</span> thermo_style custom step etotal pe ke temp press
</pre></div> thermo_modify temp effTemp
</div> </pre>
<p>See <a class="reference internal" href="compute_temp_eff.html"><span class="doc">compute temp/eff</span></a>.</p> <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><strong>Output info:</strong></p>
<p>This compute calculates a global scalar (the KE). This value can be <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> <span id="index-0"></span><h1>compute_modify command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<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 class="literal-block">
</pre></div> compute_modify compute-ID keyword value ...
</div> </pre>
<ul class="simple"> <ul class="simple">
<li>compute-ID = ID of the compute to modify</li> <li>compute-ID = ID of the compute to modify</li>
<li>one or more keyword/value pairs may be listed</li> <li>one or more keyword/value pairs may be listed</li>
@ -145,10 +145,10 @@
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<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> <pre class="literal-block">
<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> compute_modify myTemp extra 0
</pre></div> compute_modify newtemp dynamic yes extra 600
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <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 <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 energy, these lines in an input script should yield the same result
in the last 2 columns of thermo output:</p> in the last 2 columns of thermo output:</p>
<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> <pre class="literal-block">
<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> compute peratom all pe/atom
<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> compute pe all reduce sum c_peratom
</pre></div> thermo_style custom step temp etotal press pe c_pe
</div> </pre>
<div class="admonition note"> <div class="admonition note">
<p class="first admonition-title">Note</p> <p class="first admonition-title">Note</p>
<p class="last">The per-atom energy does not any Lennard-Jones tail corrections <p class="last">The per-atom energy does not any Lennard-Jones tail corrections

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@ -141,10 +141,10 @@
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<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">pressure</span> <span class="n">thermo_temp</span> <pre class="literal-block">
<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">NULL</span> <span class="n">pair</span> <span class="n">bond</span> compute 1 all pressure thermo_temp
</pre></div> compute 1 all pressure NULL pair bond
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>
@ -196,9 +196,9 @@ degrees-of-freedom divided by d = dimensionality, where the DOF value
is calcluated by the temperature compute. See the various <a class="reference internal" href="compute.html"><span class="doc">compute temperature</span></a> styles for details.</p> is calcluated by the temperature compute. See the various <a class="reference internal" href="compute.html"><span class="doc">compute temperature</span></a> styles for details.</p>
<p>A compute of this style with the ID of &#8220;thermo_press&#8221; is created when <p>A compute of this style with the ID of &#8220;thermo_press&#8221; is created when
LAMMPS starts up, as if this command were in the input script:</p> LAMMPS starts up, as if this command were in the input script:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">thermo_press</span> <span class="nb">all</span> <span class="n">pressure</span> <span class="n">thermo_temp</span> <pre class="literal-block">
</pre></div> compute thermo_press all pressure thermo_temp
</div> </pre>
<p>where &#8220;thermo_temp&#8221; is the ID of a similarly defined compute of style <p>where &#8220;thermo_temp&#8221; is the ID of a similarly defined compute of style
&#8220;temp&#8221;. See the &#8220;thermo_style&#8221; command for more details.</p> &#8220;temp&#8221;. See the &#8220;thermo_style&#8221; command for more details.</p>
<hr class="docutils" /> <hr class="docutils" />

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

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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 <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> 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> command, for example:</p>
<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> <pre class="literal-block">
<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> compute cc1 all chunk/atom molecule
<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> compute myChunk1 all property/chunk cc1 count
<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> compute myChunk2 all com/chunk cc1
</pre></div> fix 1 all ave/time 100 1 100 c_myChunk1 c_myChunk2[*] file tmp.out mode vector
</div> </pre>
<p><strong>Output info:</strong></p> <p><strong>Output info:</strong></p>
<p>This compute calculates a global vector or global array depending on <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 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>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> <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> </ul>
<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> <pre class="literal-block">
<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> x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
<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> c_ID = per-atom or local vector calculated by a compute with ID
<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> c_ID[I] = Ith column of per-atom or local array calculated by a compute with ID, I can include wildcard (see below)
<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> f_ID = per-atom or local vector calculated by a fix with ID
<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> f_ID[I] = Ith column of per-atom or local array calculated by a fix with ID, I can include wildcard (see below)
</pre></div> v_name = per-atom vector calculated by an atom-style variable with name
</div> </pre>
<ul class="simple"> <ul class="simple">
<li>zero or more keyword/args pairs may be appended</li> <li>zero or more keyword/args pairs may be appended</li>
<li>keyword = <em>replace</em></li> <li>keyword = <em>replace</em></li>
@ -168,13 +168,13 @@
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<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> <pre class="literal-block">
<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> compute 1 all reduce sum c_force
<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> compute 1 all reduce/region subbox sum c_force
<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> compute 2 all reduce min c_press[2] f_ave v_myKE
<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> compute 2 all reduce min c_press[*] f_ave v_myKE
</pre></div> compute 3 fluid reduce max c_index[1] c_index[2] c_dist replace 1 3 replace 2 3
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <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> <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 <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 be specified using a wildcard asterisk with the index to effectively
specify multiple values. This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or 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 size of the vector (for <em>mode</em> = scalar) or the &#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 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 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 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> 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> command creates a per-atom array with 6 columns:</p>
<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> <pre class="literal-block">
<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> compute myPress all stress/atom NULL
<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> compute 2 all reduce min myPress[*]
<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> compute 2 all reduce min myPress[1] myPress[2] myPress[3] &amp;
</pre></div> myPress[4] myPress[5] myPress[6]
</div> </pre>
<hr class="docutils" /> <hr class="docutils" />
<p>The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are <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 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 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> an input value from that compute.</p>
<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 <p>If a value begins with &#8220;c_&#8221;, a compute ID must follow which has been
previously defined in the input script. Computes can generate previously defined in the input script. Computes can generate
per-atom or local quantities. See the individual 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 <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 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 discussion above for how I can be specified with a wildcard asterisk
to effectively specify multiple values.</p> to effectively specify multiple values.</p>
<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 <p>If a value begins with &#8220;f_&#8221;, a fix ID must follow which has been
previously defined in the input script. Fixes can generate per-atom 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 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 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 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 I can be specified with a wildcard asterisk to effectively specify
multiple values.</p> multiple values.</p>
<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 <p>If a value begins with &#8220;v_&#8221;, a variable name must follow which has
been previously defined in the input script. It must be an 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 <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 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> 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 <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> with maximum stretch, you can do it as follows:</p>
<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> <pre class="literal-block">
<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> compute 1 all property/local batom1 batom2
<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> compute 2 all bond/local dist
<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> compute 3 all reduce max c_1[1] c_1[2] c_2 replace 1 3 replace 2 3
</pre></div> thermo_style custom step temp c_3[1] c_3[2] c_3[3]
</div> </pre>
<p>The first two input values in the compute reduce command are vectors <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 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 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

8
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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> 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 <p>Here is an example of how to use this compute to dump rigid body info
to a file:</p> to a file:</p>
<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> <pre class="literal-block">
<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> compute 1 all rigid/local myRigid mol x y z fx fy fz
</pre></div> 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]
</div> </pre>
<hr class="docutils" /> <hr class="docutils" />
<p>This section explains the rigid body attributes that can be specified.</p> <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 <p>The <em>id</em> attribute is the atomID of the atom which owns the rigid body, which is

18
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@ -157,14 +157,14 @@
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<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> <pre class="literal-block">
<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> 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
</pre></div> compute 2 all saed 0.0251 Ni Kmax 1.70 Zone 0 0 0 c 0.05 0.05 0.05 manual echo
</div> </pre>
<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> <pre class="literal-block">
<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> fix saed/vtk 1 1 1 c_1 file Al2O3_001.saed
</pre></div> fix saed/vtk 1 1 1 c_2 file Ni_000.saed
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>
@ -193,7 +193,7 @@ shown in the 2D diagram below.</p>
height="auto" height="auto"
alt=""/> alt=""/>
</a><p>For a mesh defined by the simulation domain, a rectilinear grid is </a><p>For a mesh defined by the simulation domain, a rectilinear grid is
constructed with spacing <em>c</em><a href="#id1"><span class="problematic" id="id2">*</span></a>inv(A) along each reciprocal lattice constructed with spacing <em>c</em>*inv(A) along each reciprocal lattice
axis. Where A are the vectors corresponding to the edges of the axis. Where A are the vectors corresponding to the edges of the
simulation cell. If one or two directions has non-periodic boundary simulation cell. If one or two directions has non-periodic boundary
conditions, then the spacing in these directions is defined from the conditions, then the spacing in these directions is defined from the

42
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@ -134,11 +134,11 @@
<h1>compute snav/atom command</h1> <h1>compute snav/atom command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">sna</span><span class="o">/</span><span class="n">atom</span> <span class="n">rcutfac</span> <span class="n">rfac0</span> <span class="n">twojmax</span> <span class="n">R_1</span> <span class="n">R_2</span> <span class="o">...</span> <span class="n">w_1</span> <span class="n">w_2</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span> <pre class="literal-block">
<span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">snad</span><span class="o">/</span><span class="n">atom</span> <span class="n">rcutfac</span> <span class="n">rfac0</span> <span class="n">twojmax</span> <span class="n">R_1</span> <span class="n">R_2</span> <span class="o">...</span> <span class="n">w_1</span> <span class="n">w_2</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span> compute ID group-ID sna/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
<span class="n">compute</span> <span class="n">ID</span> <span class="n">group</span><span class="o">-</span><span class="n">ID</span> <span class="n">snav</span><span class="o">/</span><span class="n">atom</span> <span class="n">rcutfac</span> <span class="n">rfac0</span> <span class="n">twojmax</span> <span class="n">R_1</span> <span class="n">R_2</span> <span class="o">...</span> <span class="n">w_1</span> <span class="n">w_2</span> <span class="o">...</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span> compute ID group-ID snad/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
</pre></div> compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
</div> </pre>
<ul class="simple"> <ul class="simple">
<li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li> <li>ID, group-ID are documented in <a class="reference internal" href="compute.html"><span class="doc">compute</span></a> command</li>
<li>sna/atom = style name of this compute command</li> <li>sna/atom = style name of this compute command</li>
@ -276,22 +276,22 @@ corresponding to a particular bispectrum component. The total number
of columns and the identities of the bispectrum component contained in of columns and the identities of the bispectrum component contained in
each column depend on the values of <em>twojmax</em> and <em>diagonal</em>, as each column depend on the values of <em>twojmax</em> and <em>diagonal</em>, as
described by the following piece of python code:</p> described by the following piece of python code:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="k">for</span> <span class="n">j1</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="n">twojmax</span><span class="o">+</span><span class="mi">1</span><span class="p">):</span> <pre class="literal-block">
<span class="k">if</span><span class="p">(</span><span class="n">diagonal</span><span class="o">==</span><span class="mi">2</span><span class="p">):</span> for j1 in range(0,twojmax+1):
<span class="nb">print</span> <span class="n">j1</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j1</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j1</span><span class="o">/</span><span class="mf">2.</span> if(diagonal==2):
<span class="k">elif</span><span class="p">(</span><span class="n">diagonal</span><span class="o">==</span><span class="mi">1</span><span class="p">):</span> print j1/2.,j1/2.,j1/2.
<span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="nb">min</span><span class="p">(</span><span class="n">twojmax</span><span class="p">,</span><span class="mi">2</span><span class="o">*</span><span class="n">j1</span><span class="p">)</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span><span class="mi">2</span><span class="p">):</span> elif(diagonal==1):
<span class="nb">print</span> <span class="n">j1</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j1</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j</span><span class="o">/</span><span class="mf">2.</span> for j in range(0,min(twojmax,2*j1)+1,2):
<span class="k">elif</span><span class="p">(</span><span class="n">diagonal</span><span class="o">==</span><span class="mi">0</span><span class="p">):</span> print j1/2.,j1/2.,j/2.
<span class="k">for</span> <span class="n">j2</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="n">j1</span><span class="o">+</span><span class="mi">1</span><span class="p">):</span> elif(diagonal==0):
<span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">j1</span><span class="o">-</span><span class="n">j2</span><span class="p">,</span><span class="nb">min</span><span class="p">(</span><span class="n">twojmax</span><span class="p">,</span><span class="n">j1</span><span class="o">+</span><span class="n">j2</span><span class="p">)</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span><span class="mi">2</span><span class="p">):</span> for j2 in range(0,j1+1):
<span class="nb">print</span> <span class="n">j1</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j2</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j</span><span class="o">/</span><span class="mf">2.</span> for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
<span class="k">elif</span><span class="p">(</span><span class="n">diagonal</span><span class="o">==</span><span class="mi">3</span><span class="p">):</span> print j1/2.,j2/2.,j/2.
<span class="k">for</span> <span class="n">j2</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="n">j1</span><span class="o">+</span><span class="mi">1</span><span class="p">):</span> elif(diagonal==3):
<span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">j1</span><span class="o">-</span><span class="n">j2</span><span class="p">,</span><span class="nb">min</span><span class="p">(</span><span class="n">twojmax</span><span class="p">,</span><span class="n">j1</span><span class="o">+</span><span class="n">j2</span><span class="p">)</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span><span class="mi">2</span><span class="p">):</span> for j2 in range(0,j1+1):
<span class="k">if</span> <span class="p">(</span><span class="n">j</span><span class="o">&gt;=</span><span class="n">j1</span><span class="p">):</span> <span class="nb">print</span> <span class="n">j1</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j2</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j</span><span class="o">/</span><span class="mf">2.</span> for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
</pre></div> if (j&gt;=j1): print j1/2.,j2/2.,j/2.
</div> </pre>
<p>Compute <em>snad/atom</em> evaluates a per-atom array. The columns are <p>Compute <em>snad/atom</em> evaluates a per-atom array. The columns are
arranged into <em>ntypes</em> blocks, listed in order of atom type <em>I</em>. Each arranged into <em>ntypes</em> blocks, listed in order of atom type <em>I</em>. Each
block contains three sub-blocks corresponding to the <em>x</em>, <em>y</em>, and <em>z</em> block contains three sub-blocks corresponding to the <em>x</em>, <em>y</em>, and <em>z</em>

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@ -234,12 +234,12 @@ d = dimension and V is the volume of the system, the result should be
-P, where P is the total pressure of the system.</p> -P, where P is the total pressure of the system.</p>
<p>These lines in an input script for a 3d system should yield that <p>These lines in an input script for a 3d system should yield that
result. I.e. the last 2 columns of thermo output will be the same:</p> result. I.e. the last 2 columns of thermo output will be the same:</p>
<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">stress</span><span class="o">/</span><span class="n">atom</span> <span class="n">NULL</span> <pre class="literal-block">
<span class="n">compute</span> <span class="n">p</span> <span class="nb">all</span> <span class="n">reduce</span> <span class="nb">sum</span> <span class="n">c_peratom</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_peratom</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_peratom</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> compute peratom all stress/atom NULL
<span class="n">variable</span> <span class="n">press</span> <span class="n">equal</span> <span class="o">-</span><span class="p">(</span><span class="n">c_p</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span><span class="o">+</span><span class="n">c_p</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span><span class="o">+</span><span class="n">c_p</span><span class="p">[</span><span class="mi">3</span><span class="p">])</span><span class="o">/</span><span class="p">(</span><span class="mi">3</span><span class="o">*</span><span class="n">vol</span><span class="p">)</span> compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
<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">v_press</span> variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
</pre></div> thermo_style custom step temp etotal press v_press
</div> </pre>
<p><strong>Output info:</strong></p> <p><strong>Output info:</strong></p>
<p>This compute calculates a per-atom array with 6 columns, which can be <p>This compute calculates a per-atom array with 6 columns, which can be
accessed by indices 1-6 by any command that uses per-atom values from accessed by indices 1-6 by any command that uses per-atom values from

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@ -140,10 +140,10 @@
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<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> <pre class="literal-block">
<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> compute oxygen_c-s all temp/cs O_core O_shell
</pre></div> compute core_shells all temp/cs cores shells
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <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 <a class="reference internal" href="thermo_modify.html"><span class="doc">thermo_modify</span></a> command, as shown in the following
example:</p> example:</p>
</div> </div>
<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> <pre class="literal-block">
<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> compute effTemp all temp/eff
<span class="n">thermo_modify</span> <span class="n">temp</span> <span class="n">effTemp</span> thermo_style custom step etotal pe ke temp press
</pre></div> thermo_modify temp effTemp
</div> </pre>
<p>A 6-component kinetic energy tensor is also calculated by this compute <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 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 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>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<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> <pre class="literal-block">
<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> compute 1 all ti lj/cut 1 v_lj v_dlj coul/long 2 v_c v_dc kspace 1 v_ks v_dks
</pre></div> compute 1 all ti lj/cut 1*3 v_lj v_dlj coul/long * v_c v_dc kspace * v_ks v_dks
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <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 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 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 <em>atype</em> argument to select multiple atom 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 &#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#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 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 leading asterisk means all types from 1 to n (inclusive). A trailing
asterisk means all types from n to N (inclusive). A middle asterisk 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>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<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> <pre class="literal-block">
<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> compute 1 all voronoi/atom
<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> compute 2 precipitate voronoi/atom surface matrix
<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> compute 3b precipitate voronoi/atom radius v_r
<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> compute 4 solute voronoi/atom only_group
<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> compute 5 defects voronoi/atom occupation
</pre></div> compute 6 all voronoi/atom neighbors yes
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <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 <p>If the <em>radius</em> keyword is specified with an atom style variable as
the argument, a poly-disperse Voronoi tessellation is the argument, a poly-disperse Voronoi tessellation is
performed. Examples for radius variables are</p> performed. Examples for radius variables are</p>
<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> <pre class="literal-block">
<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> variable r1 atom (type==1)*0.1+(type==2)*0.4
<span class="n">variable</span> <span class="n">r2</span> <span class="n">atom</span> <span class="n">c_radius</span> compute radius all property/atom radius
</pre></div> variable r2 atom c_radius
</div> </pre>
<p>Here v_r1 specifies a per-type radius of 0.1 units for type 1 atoms <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 and 0.4 units for type 2 atoms, and v_r2 accesses the radius property
present in atom_style sphere for granular models.</p> 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 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 <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> all the Voronoi neighbors in a system:</p>
<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> <pre class="literal-block">
<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> compute 6 all voronoi/atom neighbors yes
</pre></div> dump d2 all local 1 dump.neighbors index c_6[1] c_6[2] c_6[3]
</div> </pre>
<p>If the <em>face_threshold</em> keyword is used, then only faces <p>If the <em>face_threshold</em> keyword is used, then only faces
with areas greater than the threshold are stored.</p> with areas greater than the threshold are stored.</p>
<hr class="docutils" /> <hr class="docutils" />

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@ -159,10 +159,10 @@
<span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">xrd</span> <span class="mf">1.541838</span> <span class="n">Al</span> <span class="n">O</span> <span class="mi">2</span><span class="n">Theta</span> <span class="mi">10</span> <span class="mi">100</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">LP</span> <span class="mi">1</span> <span class="n">manual</span> <span class="n">compute</span> <span class="mi">2</span> <span class="nb">all</span> <span class="n">xrd</span> <span class="mf">1.541838</span> <span class="n">Al</span> <span class="n">O</span> <span class="mi">2</span><span class="n">Theta</span> <span class="mi">10</span> <span class="mi">100</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">LP</span> <span class="mi">1</span> <span class="n">manual</span>
</pre></div> </pre></div>
</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">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="mf">0.087</span> <span class="mf">0.87</span> <span class="mi">250</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">mode</span> <span class="n">vector</span> <span class="n">file</span> <span class="n">Rad2Theta</span><span class="o">.</span><span class="n">xrd</span> <pre class="literal-block">
<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="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">250</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> <span class="n">mode</span> <span class="n">vector</span> <span class="n">file</span> <span class="n">Deg2Theta</span><span class="o">.</span><span class="n">xrd</span> fix 1 all ave/histo/weight 1 1 1 0.087 0.87 250 c_1[1] c_1[2] mode vector file Rad2Theta.xrd
</pre></div> fix 2 all ave/histo/weight 1 1 1 10 100 250 c_2[1] c_2[2] mode vector file Deg2Theta.xrd
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>
@ -196,7 +196,7 @@ shown in the 2D diagram below.</p>
height="auto" height="auto"
alt=""/> alt=""/>
</a><p>For a mesh defined by the simulation domain, a rectilinear grid is </a><p>For a mesh defined by the simulation domain, a rectilinear grid is
constructed with spacing <em>c</em><a href="#id1"><span class="problematic" id="id2">*</span></a>inv(A) along each reciprocal lattice constructed with spacing <em>c</em>*inv(A) along each reciprocal lattice
axis. Where A are the vectors corresponding to the edges of the axis. Where A are the vectors corresponding to the edges of the
simulation cell. If one or two directions has non-periodic boundary simulation cell. If one or two directions has non-periodic boundary
conditions, then the spacing in these directions is defined from the conditions, then the spacing in these directions is defined from the

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@ -128,9 +128,9 @@
<span id="index-0"></span><h1>create_atoms command</h1> <span id="index-0"></span><h1>create_atoms command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">create_atoms</span> <span class="nb">type</span> <span class="n">style</span> <span class="n">args</span> <span class="n">keyword</span> <span class="n">values</span> <span class="o">...</span> <pre class="literal-block">
</pre></div> create_atoms type style args keyword values ...
</div> </pre>
<ul class="simple"> <ul class="simple">
<li>type = atom type (1-Ntypes) of atoms to create (offset for molecule creation)</li> <li>type = atom type (1-Ntypes) of atoms to create (offset for molecule creation)</li>
<li>style = <em>box</em> or <em>region</em> or <em>single</em> or <em>random</em></li> <li>style = <em>box</em> or <em>region</em> or <em>single</em> or <em>random</em></li>
@ -172,12 +172,12 @@
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">create_atoms</span> <span class="mi">1</span> <span class="n">box</span> <pre class="literal-block">
<span class="n">create_atoms</span> <span class="mi">3</span> <span class="n">region</span> <span class="n">regsphere</span> <span class="n">basis</span> <span class="mi">2</span> <span class="mi">3</span> create_atoms 1 box
<span class="n">create_atoms</span> <span class="mi">3</span> <span class="n">single</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mi">5</span> create_atoms 3 region regsphere basis 2 3
<span class="n">create_atoms</span> <span class="mi">1</span> <span class="n">box</span> <span class="n">var</span> <span class="n">v</span> <span class="nb">set</span> <span class="n">x</span> <span class="n">xpos</span> <span class="nb">set</span> <span class="n">y</span> <span class="n">ypos</span> create_atoms 3 single 0 0 5
</pre></div> create_atoms 1 box var v set x xpos set y ypos
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>
@ -328,19 +328,19 @@ the sinusoid would appear to be &#8220;smoother&#8221;. Also note the use of th
&#8220;xlat&#8221; and &#8220;ylat&#8221; <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> keywords which &#8220;xlat&#8221; and &#8220;ylat&#8221; <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> keywords which
converts lattice spacings to distance. Click on the image for a converts lattice spacings to distance. Click on the image for a
larger version.</p> larger version.</p>
<div class="highlight-default"><div class="highlight"><pre><span></span>variable x equal 100 <pre class="literal-block">
variable x equal 100
variable y equal 25 variable y equal 25
lattice hex 0.8442 lattice hex 0.8442
region box block 0 $x 0 $y -0.5 0.5 region box block 0 $x 0 $y -0.5 0.5
create_box 1 box create_box 1 box
</pre></div> </pre>
</div> <pre class="literal-block">
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">xx</span> <span class="n">equal</span> <span class="mf">0.0</span> variable xx equal 0.0
<span class="n">variable</span> <span class="n">yy</span> <span class="n">equal</span> <span class="mf">0.0</span> variable yy equal 0.0
<span class="n">variable</span> <span class="n">v</span> <span class="n">equal</span> <span class="s2">&quot;(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) &gt; 0.0&quot;</span> variable v equal &quot;(0.2*v_y*ylat * cos(v_xx/xlat * 2.0*PI*4.0/v_x) + 0.5*v_y*ylat - v_yy) &gt; 0.0&quot;
<span class="n">create_atoms</span> <span class="mi">1</span> <span class="n">box</span> <span class="n">var</span> <span class="n">v</span> <span class="nb">set</span> <span class="n">x</span> <span class="n">xx</span> <span class="nb">set</span> <span class="n">y</span> <span class="n">yy</span> create_atoms 1 box var v set x xx set y yy
</pre></div> </pre>
</div>
<a class="" <a class=""
data-lightbox="group-default" data-lightbox="group-default"
href="_images/sinusoid.jpg" href="_images/sinusoid.jpg"

20
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@ -128,9 +128,9 @@
<span id="index-0"></span><h1>delete_bonds command</h1> <span id="index-0"></span><h1>delete_bonds command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<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 class="literal-block">
</pre></div> delete_bonds group-ID style arg keyword ...
</div> </pre>
<ul> <ul>
<li><p class="first">group-ID = group ID</p> <li><p class="first">group-ID = group ID</p>
</li> </li>
@ -157,12 +157,12 @@
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<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> <pre class="literal-block">
<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> delete_bonds frozen multi remove
<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> delete_bonds all atom 4 special
<span class="n">delete_bonds</span> <span class="nb">all</span> <span class="n">stats</span> delete_bonds all bond 0*3 special
</pre></div> delete_bonds all stats
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <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 (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 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 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;<em>n&#8221; or &#8220;n</em>&#8221; or specify a range of 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 types, then an asterisk with no numeric &#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 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 types from 0 to n (inclusive). A trailing asterisk means all types

18
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@ -137,18 +137,18 @@
<h1>dihedral_style charmm/omp command</h1> <h1>dihedral_style charmm/omp command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">charmm</span> <pre class="literal-block">
</pre></div> dihedral_style charmm
</div> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">charmm</span> <pre class="literal-block">
<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mf">0.2</span> <span class="mi">1</span> <span class="mi">180</span> <span class="mf">1.0</span> dihedral_style charmm
<span class="n">dihedral_coeff</span> <span class="mi">2</span> <span class="mf">1.8</span> <span class="mi">1</span> <span class="mi">0</span> <span class="mf">1.0</span> dihedral_coeff 1 0.2 1 180 1.0
<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mf">3.1</span> <span class="mi">2</span> <span class="mi">180</span> <span class="mf">0.5</span> dihedral_coeff 2 1.8 1 0 1.0
</pre></div> dihedral_coeff 1 3.1 2 180 0.5
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>

24
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@ -131,21 +131,21 @@
<h1>dihedral_style class2/omp command</h1> <h1>dihedral_style class2/omp command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">class2</span> <pre class="literal-block">
</pre></div> dihedral_style class2
</div> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">class2</span> <pre class="literal-block">
<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mi">100</span> <span class="mi">75</span> <span class="mi">100</span> <span class="mi">70</span> <span class="mi">80</span> <span class="mi">60</span> dihedral_style class2
<span class="n">dihedral_coeff</span> <span class="o">*</span> <span class="n">mbt</span> <span class="mf">3.5945</span> <span class="mf">0.1704</span> <span class="o">-</span><span class="mf">0.5490</span> <span class="mf">1.5228</span> dihedral_coeff 1 100 75 100 70 80 60
<span class="n">dihedral_coeff</span> <span class="o">*</span> <span class="n">ebt</span> <span class="mf">0.3417</span> <span class="mf">0.3264</span> <span class="o">-</span><span class="mf">0.9036</span> <span class="mf">0.1368</span> <span class="mf">0.0</span> <span class="o">-</span><span class="mf">0.8080</span> <span class="mf">1.0119</span> <span class="mf">1.1010</span> dihedral_coeff * mbt 3.5945 0.1704 -0.5490 1.5228
<span class="n">dihedral_coeff</span> <span class="mi">2</span> <span class="n">at</span> <span class="mf">0.0</span> <span class="o">-</span><span class="mf">0.1850</span> <span class="o">-</span><span class="mf">0.7963</span> <span class="o">-</span><span class="mf">2.0220</span> <span class="mf">0.0</span> <span class="o">-</span><span class="mf">0.3991</span> <span class="mf">110.2453</span> <span class="mf">105.1270</span> dihedral_coeff * ebt 0.3417 0.3264 -0.9036 0.1368 0.0 -0.8080 1.0119 1.1010
<span class="n">dihedral_coeff</span> <span class="o">*</span> <span class="n">aat</span> <span class="o">-</span><span class="mf">13.5271</span> <span class="mf">110.2453</span> <span class="mf">105.1270</span> dihedral_coeff 2 at 0.0 -0.1850 -0.7963 -2.0220 0.0 -0.3991 110.2453 105.1270
<span class="n">dihedral_coeff</span> <span class="o">*</span> <span class="n">bb13</span> <span class="mf">0.0</span> <span class="mf">1.0119</span> <span class="mf">1.1010</span> dihedral_coeff * aat -13.5271 110.2453 105.1270
</pre></div> dihedral_coeff * bb13 0.0 1.0119 1.1010
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>

14
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@ -131,16 +131,16 @@
<h1>dihedral_style cosine/shift/exp/omp command</h1> <h1>dihedral_style cosine/shift/exp/omp command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">shift</span><span class="o">/</span><span class="n">exp</span> <pre class="literal-block">
</pre></div> dihedral_style cosine/shift/exp
</div> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">cosine</span><span class="o">/</span><span class="n">shift</span><span class="o">/</span><span class="n">exp</span> <pre class="literal-block">
<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mf">10.0</span> <span class="mf">45.0</span> <span class="mf">2.0</span> dihedral_style cosine/shift/exp
</pre></div> dihedral_coeff 1 10.0 45.0 2.0
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>

14
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@ -131,16 +131,16 @@
<h1>dihedral_style fourier/omp command</h1> <h1>dihedral_style fourier/omp command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">fourier</span> <pre class="literal-block">
</pre></div> dihedral_style fourier
</div> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">fourier</span> <pre class="literal-block">
<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mi">3</span> <span class="o">-</span><span class="mf">0.846200</span> <span class="mi">3</span> <span class="mf">0.0</span> <span class="mf">7.578800</span> <span class="mi">1</span> <span class="mi">0</span> <span class="mf">0.138000</span> <span class="mi">2</span> <span class="o">-</span><span class="mf">180.0</span> dihedral_style fourier
</pre></div> dihedral_coeff 1 3 -0.846200 3 0.0 7.578800 1 0 0.138000 2 -180.0
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>

14
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@ -134,16 +134,16 @@
<h1>dihedral_style harmonic/omp command</h1> <h1>dihedral_style harmonic/omp command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">harmonic</span> <pre class="literal-block">
</pre></div> dihedral_style harmonic
</div> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">harmonic</span> <pre class="literal-block">
<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mf">80.0</span> <span class="mi">1</span> <span class="mi">2</span> dihedral_style harmonic
</pre></div> dihedral_coeff 1 80.0 1 2
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>

14
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@ -131,16 +131,16 @@
<h1>dihedral_style helix/omp command</h1> <h1>dihedral_style helix/omp command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">helix</span> <pre class="literal-block">
</pre></div> dihedral_style helix
</div> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">helix</span> <pre class="literal-block">
<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mf">80.0</span> <span class="mf">100.0</span> <span class="mf">40.0</span> dihedral_style helix
</pre></div> dihedral_coeff 1 80.0 100.0 40.0
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>

14
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@ -131,16 +131,16 @@
<h1>dihedral_style multi/harmonic/omp command</h1> <h1>dihedral_style multi/harmonic/omp command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">multi</span><span class="o">/</span><span class="n">harmonic</span> <pre class="literal-block">
</pre></div> dihedral_style multi/harmonic
</div> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">multi</span><span class="o">/</span><span class="n">harmonic</span> <pre class="literal-block">
<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mi">20</span> <span class="mi">20</span> <span class="mi">20</span> <span class="mi">20</span> <span class="mi">20</span> dihedral_style multi/harmonic
</pre></div> dihedral_coeff 1 20 20 20 20 20
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>

14
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@ -131,16 +131,16 @@
<h1>dihedral_style nharmonic/omp command</h1> <h1>dihedral_style nharmonic/omp command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">nharmonic</span> <pre class="literal-block">
</pre></div> dihedral_style nharmonic
</div> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">nharmonic</span> <pre class="literal-block">
<span class="n">dihedral_coeff</span> <span class="mi">3</span> <span class="mf">10.0</span> <span class="mf">20.0</span> <span class="mf">30.0</span> dihedral_style nharmonic
</pre></div> dihedral_coeff 3 10.0 20.0 30.0
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>

18
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@ -137,18 +137,18 @@
<h1>dihedral_style opls/omp command</h1> <h1>dihedral_style opls/omp command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">opls</span> <pre class="literal-block">
</pre></div> dihedral_style opls
</div> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">opls</span> <pre class="literal-block">
<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mf">1.740</span> <span class="o">-</span><span class="mf">0.157</span> <span class="mf">0.279</span> <span class="mf">0.00</span> <span class="c1"># CT-CT-CT-CT</span> dihedral_style opls
<span class="n">dihedral_coeff</span> <span class="mi">2</span> <span class="mf">0.000</span> <span class="mf">0.000</span> <span class="mf">0.366</span> <span class="mf">0.000</span> <span class="c1"># CT-CT-CT-HC</span> dihedral_coeff 1 1.740 -0.157 0.279 0.00 # CT-CT-CT-CT
<span class="n">dihedral_coeff</span> <span class="mi">3</span> <span class="mf">0.000</span> <span class="mf">0.000</span> <span class="mf">0.318</span> <span class="mf">0.000</span> <span class="c1"># HC-CT-CT-HC</span> dihedral_coeff 2 0.000 0.000 0.366 0.000 # CT-CT-CT-HC
</pre></div> dihedral_coeff 3 0.000 0.000 0.318 0.000 # HC-CT-CT-HC
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>

14
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@ -131,16 +131,16 @@
<h1>dihedral_style quadratic/omp command</h1> <h1>dihedral_style quadratic/omp command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">quadratic</span> <pre class="literal-block">
</pre></div> dihedral_style quadratic
</div> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">quadratic</span> <pre class="literal-block">
<span class="n">dihedral_coeff</span> <span class="mf">100.0</span> <span class="mf">80.0</span> dihedral_style quadratic
</pre></div> dihedral_coeff 100.0 80.0
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>

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@ -128,18 +128,18 @@
<span id="index-0"></span><h1>dihedral_style spherical command</h1> <span id="index-0"></span><h1>dihedral_style spherical command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">spherical</span> <pre class="literal-block">
</pre></div> dihedral_style spherical
</div> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">286.1</span> <span class="mi">1</span> <span class="mi">124</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mf">90.0</span> <span class="mi">0</span> <span class="mi">1</span> <span class="mf">90.0</span> <span class="mi">0</span> <pre class="literal-block">
<span class="n">dihedral_coeff</span> <span class="mi">1</span> <span class="mi">3</span> <span class="mf">286.1</span> <span class="mi">1</span> <span class="mi">114</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">90</span> <span class="mi">0</span> <span class="mi">1</span> <span class="mf">90.0</span> <span class="mi">0</span> <span class="o">&amp;</span> dihedral_coeff 1 1 286.1 1 124 1 1 90.0 0 1 90.0 0
<span class="mf">17.3</span> <span class="mi">0</span> <span class="mf">0.0</span> <span class="mi">0</span> <span class="mi">1</span> <span class="mi">158</span> <span class="mi">1</span> <span class="mi">0</span> <span class="mf">0.0</span> <span class="mi">0</span> <span class="o">&amp;</span> dihedral_coeff 1 3 286.1 1 114 1 1 90 0 1 90.0 0 &amp;
<span class="mf">15.1</span> <span class="mi">0</span> <span class="mf">0.0</span> <span class="mi">0</span> <span class="mi">0</span> <span class="mf">0.0</span> <span class="mi">0</span> <span class="mi">1</span> <span class="mf">167.3</span> <span class="mi">1</span> 17.3 0 0.0 0 1 158 1 0 0.0 0 &amp;
</pre></div> 15.1 0 0.0 0 0 0.0 0 1 167.3 1
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>

16
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@ -128,20 +128,20 @@
<span id="index-0"></span><h1>dihedral_style command</h1> <span id="index-0"></span><h1>dihedral_style command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">style</span> <pre class="literal-block">
</pre></div> dihedral_style style
</div> </pre>
<ul class="simple"> <ul class="simple">
<li>style = <em>none</em> or <em>hybrid</em> or <em>charmm</em> or <em>class2</em> or <em>harmonic</em> or <em>helix</em> or <em>multi/harmonic</em> or <em>opls</em></li> <li>style = <em>none</em> or <em>hybrid</em> or <em>charmm</em> or <em>class2</em> or <em>harmonic</em> or <em>helix</em> or <em>multi/harmonic</em> or <em>opls</em></li>
</ul> </ul>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dihedral_style</span> <span class="n">harmonic</span> <pre class="literal-block">
<span class="n">dihedral_style</span> <span class="n">multi</span><span class="o">/</span><span class="n">harmonic</span> dihedral_style harmonic
<span class="n">dihedral_style</span> <span class="n">hybrid</span> <span class="n">harmonic</span> <span class="n">charmm</span> dihedral_style multi/harmonic
</pre></div> dihedral_style hybrid harmonic charmm
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>

46
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@ -131,9 +131,9 @@
<h1>dihedral_style table/omp command</h1> <h1>dihedral_style table/omp command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<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 class="literal-block">
</pre></div> dihedral_style table style Ntable
</div> </pre>
<ul class="simple"> <ul class="simple">
<li>style = <em>linear</em> or <em>spline</em> = method of interpolation</li> <li>style = <em>linear</em> or <em>spline</em> = method of interpolation</li>
<li>Ntable = size of the internal lookup table</li> <li>Ntable = size of the internal lookup table</li>
@ -141,12 +141,12 @@
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<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> <pre class="literal-block">
<span class="n">dihedral_style</span> <span class="n">table</span> <span class="n">linear</span> <span class="mi">1000</span> dihedral_style table spline 400
<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> dihedral_style table linear 1000
<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> dihedral_coeff 1 file.table DIH_TABLE1
</pre></div> dihedral_coeff 2 file.table DIH_TABLE2
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <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> <div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Table of the potential and its negative derivative</span>
</pre></div> </pre></div>
</div> </div>
<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> <pre class="literal-block">
<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> DIH_TABLE1 (keyword is the first text on line)
<span class="p">(</span><span class="n">blank</span> <span class="n">line</span><span class="p">)</span> N 30 DEGREES (N, NOF, DEGREES, RADIANS, CHECKU/F)
<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> (blank line)
<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> 1 -168.0 -1.40351172223 0.0423346818422
<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> 2 -156.0 -1.70447981034 0.00811786522531
<span class="o">...</span> 3 -144.0 -1.62956100432 -0.0184129719987
<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> 30 180.0 -0.707106781187 0.0719306095245
</div> </pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Example 2: table of the potential. Forces omitted</span> <div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Example 2: table of the potential. Forces omitted</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">DIH_TABLE2</span> <pre class="literal-block">
<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> DIH_TABLE2
</pre></div> N 30 NOF CHECKU testU.dat CHECKF testF.dat
</div> </pre>
<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> <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">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> <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>

62
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@ -239,19 +239,19 @@ i_name = per-atom integer vector with name, managed by fix property/atom
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<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> <pre class="literal-block">
<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> dump myDump all atom 100 dump.atom
<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> dump myDump all atom/mpiio 100 dump.atom.mpiio
<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> dump myDump all atom/gz 100 dump.atom.gz
<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> dump 2 subgroup atom 50 dump.run.bin
<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> dump 2 subgroup atom 50 dump.run.mpiio.bin
<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> dump 4a all custom 100 dump.myforce.* id type x y vx fx
<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> dump 4b flow custom 100 dump.%.myforce id type c_myF[3] v_ke
<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> dump 4b flow custom 100 dump.%.myforce id type c_myF[*] v_ke
<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> dump 2 inner cfg 10 dump.snap.*.cfg mass type xs ys zs vx vy vz
<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> dump snap all cfg 100 dump.config.*.cfg mass type xs ys zs id type c_Stress[2]
</pre></div> dump 1 all xtc 1000 file.xtc
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <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, bounding box which encloses the triclinic simulation box is output,
along with the 3 tilt factors (xy, xz, yz) of the triclinic box, along with the 3 tilt factors (xy, xz, yz) of the triclinic box,
formatted as follows:</p> formatted as follows:</p>
<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> <pre class="literal-block">
<span class="n">xlo_bound</span> <span class="n">xhi_bound</span> <span class="n">xy</span> ITEM: BOX BOUNDS xy xz yz xx yy zz
<span class="n">ylo_bound</span> <span class="n">yhi_bound</span> <span class="n">xz</span> xlo_bound xhi_bound xy
<span class="n">zlo_bound</span> <span class="n">zhi_bound</span> <span class="n">yz</span> ylo_bound yhi_bound xz
</pre></div> zlo_bound zhi_bound yz
</div> </pre>
<p>The presence of the text &#8220;xy xz yz&#8221; in the ITEM line indicates that <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. the 3 tilt factors will be included on each of the 3 following lines.
This bounding box is convenient for many visualization programs. The 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 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 <em>local</em> styles, the bracketed index I can be specified using a
wildcard asterisk with the index to effectively specify multiple wildcard asterisk with the index to effectively 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 values. This takes the form &#8220;*&#8221; or &#8220;*n&#8221; or &#8220;n*&#8221; or &#8220;m*n&#8221;. If N = the
size of the vector (for <em>mode</em> = scalar) or the number of columns in 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 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 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 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> 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> command creates a per-atom array with 6 columns:</p>
<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> <pre class="literal-block">
<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> compute myPress all stress/atom NULL
<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> dump 2 all custom 100 tmp.dump id myPress[*]
<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> dump 2 all custom 100 tmp.dump id myPress[1] myPress[2] myPress[3] &amp;
</pre></div> myPress[4] myPress[5] myPress[6]
</div> </pre>
<hr class="docutils" /> <hr class="docutils" />
<p>This section explains the local attributes that can be specified as <p>This section explains the local attributes that can be specified as
part of the <em>local</em> style.</p> part of the <em>local</em> style.</p>
@ -598,11 +598,11 @@ be specified with a wildcard asterisk to effectively specify multiple
values.</p> values.</p>
<p>Here is an example of how to dump bond info for a system, including <p>Here is an example of how to dump bond info for a system, including
the distance and energy of each bond:</p> the distance and energy of each bond:</p>
<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> <pre class="literal-block">
<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> compute 1 all property/local batom1 batom2 btype
<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> compute 2 all bond/local dist eng
</pre></div> dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2]
</div> </pre>
<hr class="docutils" /> <hr class="docutils" />
<p>This section explains the atom attributes that can be specified as <p>This section explains the atom attributes that can be specified as
part of the <em>custom</em> and <em>cfg</em> styles.</p> part of the <em>custom</em> and <em>cfg</em> styles.</p>

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@ -182,15 +182,15 @@ v_name = per-atom vector calculated by an atom-style variable with name
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<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> <pre class="literal-block">
<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> dump dmpvtk all custom/vtk 100 dump*.myforce.vtk id type vx fx
<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> dump dmpvtp flow custom/vtk 100 dump*.%.displace.vtp id type c_myD[1] c_myD[2] c_myD[3] v_ke
</pre></div> dump e_data all custom/vtk 100 dump*.vtu id type spin eradius fx fy fz eforce
</div> </pre>
<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 <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 uses the VTK library to write data to VTK simple legacy or XML format
depending on the filename extension specified. This can be either depending on the filename extension specified. This can be either
<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, <em>*.vtk</em> for the legacy format or <em>*.vtp</em> and <em>*.vtu</em>, 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 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 description of these formats. Since this naming convention conflicts
with the way binary output is usually specified (see below), with the way binary output is usually specified (see below),

48
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@ -206,14 +206,14 @@
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">dump</span> <span class="n">d0</span> <span class="nb">all</span> <span class="n">image</span> <span class="mi">100</span> <span class="n">dump</span><span class="o">.*.</span><span class="n">jpg</span> <span class="nb">type</span> <span class="nb">type</span> <pre class="literal-block">
<span class="n">dump</span> <span class="n">d1</span> <span class="n">mobile</span> <span class="n">image</span> <span class="mi">500</span> <span class="n">snap</span><span class="o">.*.</span><span class="n">png</span> <span class="n">element</span> <span class="n">element</span> <span class="n">ssao</span> <span class="n">yes</span> <span class="mi">4539</span> <span class="mf">0.6</span> dump d0 all image 100 dump.*.jpg type type
<span class="n">dump</span> <span class="n">d2</span> <span class="nb">all</span> <span class="n">image</span> <span class="mi">200</span> <span class="n">img</span><span class="o">-*.</span><span class="n">ppm</span> <span class="nb">type</span> <span class="nb">type</span> <span class="n">zoom</span> <span class="mf">2.5</span> <span class="n">adiam</span> <span class="mf">1.5</span> <span class="n">size</span> <span class="mi">1280</span> <span class="mi">720</span> dump d1 mobile image 500 snap.*.png element element ssao yes 4539 0.6
<span class="n">dump</span> <span class="n">m0</span> <span class="nb">all</span> <span class="n">movie</span> <span class="mi">1000</span> <span class="n">movie</span><span class="o">.</span><span class="n">mpg</span> <span class="nb">type</span> <span class="nb">type</span> <span class="n">size</span> <span class="mi">640</span> <span class="mi">480</span> dump d2 all image 200 img-*.ppm type type zoom 2.5 adiam 1.5 size 1280 720
<span class="n">dump</span> <span class="n">m1</span> <span class="nb">all</span> <span class="n">movie</span> <span class="mi">1000</span> <span class="n">movie</span><span class="o">.</span><span class="n">avi</span> <span class="nb">type</span> <span class="nb">type</span> <span class="n">size</span> <span class="mi">640</span> <span class="mi">480</span> dump m0 all movie 1000 movie.mpg type type size 640 480
<span class="n">dump</span> <span class="n">m2</span> <span class="nb">all</span> <span class="n">movie</span> <span class="mi">100</span> <span class="n">movie</span><span class="o">.</span><span class="n">m4v</span> <span class="nb">type</span> <span class="nb">type</span> <span class="n">zoom</span> <span class="mf">1.8</span> <span class="n">adiam</span> <span class="n">v_value</span> <span class="n">size</span> <span class="mi">1280</span> <span class="mi">720</span> dump m1 all movie 1000 movie.avi type type size 640 480
</pre></div> dump m2 all movie 100 movie.m4v type type zoom 1.8 adiam v_value size 1280 720
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>
@ -310,7 +310,7 @@ atoms rendered in the image. They can be any atom attribute defined
for the <a class="reference internal" href="dump.html"><span class="doc">dump custom</span></a> command, including <em>type</em> and for the <a class="reference internal" href="dump.html"><span class="doc">dump custom</span></a> command, including <em>type</em> and
<em>element</em>. This includes per-atom quantities calculated by a <em>element</em>. This includes per-atom quantities calculated by a
<a class="reference internal" href="compute.html"><span class="doc">compute</span></a>, <a class="reference internal" href="fix.html"><span class="doc">fix</span></a>, or <a class="reference internal" href="variable.html"><span class="doc">variable</span></a>, <a class="reference internal" href="compute.html"><span class="doc">compute</span></a>, <a class="reference internal" href="fix.html"><span class="doc">fix</span></a>, or <a class="reference internal" href="variable.html"><span class="doc">variable</span></a>,
which are prefixed by &#8220;<a href="#id9"><span class="problematic" id="id10">c_</span></a>&#8221;, &#8220;<a href="#id11"><span class="problematic" id="id12">f_</span></a>&#8221;, or &#8220;<a href="#id13"><span class="problematic" id="id14">v_</span></a>&#8221; respectively. Note that the which are prefixed by &#8220;c_&#8221;, &#8220;f_&#8221;, or &#8220;v_&#8221; respectively. Note that the
<em>diameter</em> setting can be overridden with a numeric value applied to <em>diameter</em> setting can be overridden with a numeric value applied to
all atoms by the optional <em>adiam</em> keyword.</p> all atoms by the optional <em>adiam</em> keyword.</p>
<p>If <em>type</em> is specified for the <em>color</em> setting, then the color of each <p>If <em>type</em> is specified for the <em>color</em> setting, then the color of each
@ -545,9 +545,9 @@ plane perpendicular to the view vector implied by the <em>theta</em> and
<em>pni</em> values, and which is also in the plane defined by the view <em>pni</em> values, and which is also in the plane defined by the view
vector and user-specified up vector. Thus this internal vector is vector and user-specified up vector. Thus this internal vector is
computed from the user-specified <em>up</em> vector as</p> computed from the user-specified <em>up</em> vector as</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">up_internal</span> <span class="o">=</span> <span class="n">view</span> <span class="n">cross</span> <span class="p">(</span><span class="n">up</span> <span class="n">cross</span> <span class="n">view</span><span class="p">)</span> <pre class="literal-block">
</pre></div> up_internal = view cross (up cross view)
</div> </pre>
<p>This means the only restriction on the specified <em>up</em> vector is that <p>This means the only restriction on the specified <em>up</em> vector is that
it cannot be parallel to the <em>view</em> vector, implied by the <em>theta</em> and it cannot be parallel to the <em>view</em> vector, implied by the <em>theta</em> and
<em>phi</em> values.</p> <em>phi</em> values.</p>
@ -619,10 +619,10 @@ MPEG or other movie file you can use:</p>
</ol> </ol>
</li> </li>
</ul> </ul>
<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">jpg</span> <span class="n">foo</span><span class="o">.</span><span class="n">gif</span> <pre class="literal-block">
<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">ppm</span> <span class="n">foo</span><span class="o">.</span><span class="n">mpg</span> % convert *.jpg foo.gif
</pre></div> % convert -loop 1 *.ppm foo.mpg
</div> </pre>
<p>Animated GIF files from ImageMagick are unoptimized. You can use a <p>Animated GIF files from ImageMagick are unoptimized. You can use a
program like gifsicle to optimize and massively shrink them. program like gifsicle to optimize and massively shrink them.
MPEG files created by ImageMagick are in MPEG-1 format with rather MPEG files created by ImageMagick are in MPEG-1 format with rather
@ -635,7 +635,7 @@ inefficient compression and low quality.</p>
</ul> </ul>
<p>Select &#8220;Open Image Sequence&#8221; under the File menu Load the images into <p>Select &#8220;Open Image Sequence&#8221; under the File menu Load the images into
QuickTime to animate them Select &#8220;Export&#8221; under the File menu Save the QuickTime to animate them Select &#8220;Export&#8221; under the File menu Save the
movie as a QuickTime movie (<a href="#id7"><span class="problematic" id="id8">*</span></a>.mov) or in another format. QuickTime movie as a QuickTime movie (*.mov) or in another format. QuickTime
can generate very high quality and efficiently compressed movie can generate very high quality and efficiently compressed movie
files. Some of the supported formats require to buy a license and some files. Some of the supported formats require to buy a license and some
are not readable on all platforms until specific runtime libraries are are not readable on all platforms until specific runtime libraries are
@ -648,10 +648,10 @@ installed.</p>
</ul> </ul>
<p>FFmpeg is a command line tool that is available on many platforms and <p>FFmpeg is a command line tool that is available on many platforms and
allows extremely flexible encoding and decoding of movies.</p> allows extremely flexible encoding and decoding of movies.</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">cat</span> <span class="n">snap</span><span class="o">.*.</span><span class="n">jpg</span> <span class="o">|</span> <span class="n">ffmpeg</span> <span class="o">-</span><span class="n">y</span> <span class="o">-</span><span class="n">f</span> <span class="n">image2pipe</span> <span class="o">-</span><span class="n">c</span><span class="p">:</span><span class="n">v</span> <span class="n">mjpeg</span> <span class="o">-</span><span class="n">i</span> <span class="o">-</span> <span class="o">-</span><span class="n">b</span><span class="p">:</span><span class="n">v</span> <span class="mi">2000</span><span class="n">k</span> <span class="n">movie</span><span class="o">.</span><span class="n">m4v</span> <pre class="literal-block">
<span class="n">cat</span> <span class="n">snap</span><span class="o">.*.</span><span class="n">ppm</span> <span class="o">|</span> <span class="n">ffmpeg</span> <span class="o">-</span><span class="n">y</span> <span class="o">-</span><span class="n">f</span> <span class="n">image2pipe</span> <span class="o">-</span><span class="n">c</span><span class="p">:</span><span class="n">v</span> <span class="n">ppm</span> <span class="o">-</span><span class="n">i</span> <span class="o">-</span> <span class="o">-</span><span class="n">b</span><span class="p">:</span><span class="n">v</span> <span class="mi">2400</span><span class="n">k</span> <span class="n">movie</span><span class="o">.</span><span class="n">avi</span> cat snap.*.jpg | ffmpeg -y -f image2pipe -c:v mjpeg -i - -b:v 2000k movie.m4v
</pre></div> cat snap.*.ppm | ffmpeg -y -f image2pipe -c:v ppm -i - -b:v 2400k movie.avi
</div> </pre>
<p>Frontends for FFmpeg exist for multiple platforms. For more <p>Frontends for FFmpeg exist for multiple platforms. For more
information see the <a class="reference external" href="http://www.ffmpeg.org/">FFmpeg homepage</a></p> information see the <a class="reference external" href="http://www.ffmpeg.org/">FFmpeg homepage</a></p>
<hr class="docutils" /> <hr class="docutils" />
@ -678,9 +678,9 @@ variety of file formats and decoders.</li>
<a class="reference external" href="http://www.sandia.gov/~sjplimp/pizza/doc/animate.html">animate tool</a>, <a class="reference external" href="http://www.sandia.gov/~sjplimp/pizza/doc/animate.html">animate tool</a>,
which works directly on a series of image files.</li> which works directly on a series of image files.</li>
</ul> </ul>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">a</span> <span class="o">=</span> <span class="n">animate</span><span class="p">(</span><span class="s2">&quot;foo*.jpg&quot;</span><span class="p">)</span> <pre class="literal-block">
</pre></div> a = animate(&quot;foo*.jpg&quot;)
</div> </pre>
<ul class="simple"> <ul class="simple">
<li>d) QuickTime and other Windows- or MacOS-based media players can <li>d) QuickTime and other Windows- or MacOS-based media players can
obviously play movie files directly. Similarly for corresponding tools obviously play movie files directly. Similarly for corresponding tools

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@ -128,9 +128,9 @@
<span id="index-0"></span><h1>dump_modify command</h1> <span id="index-0"></span><h1>dump_modify command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<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 class="literal-block">
</pre></div> dump_modify dump-ID keyword values ...
</div> </pre>
<ul class="simple"> <ul class="simple">
<li>dump-ID = ID of dump to modify</li> <li>dump-ID = ID of dump to modify</li>
<li>one or more keyword/value pairs may be appended</li> <li>one or more keyword/value pairs may be appended</li>
@ -228,16 +228,16 @@
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<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> <pre class="literal-block">
<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> dump_modify 1 format line &quot;%d %d %20.15g %g %g&quot; scale yes
<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> dump_modify 1 format float %20.15g scale yes
<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> dump_modify myDump image yes scale no flush yes
<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> dump_modify 1 region mySphere thresh x &lt; 0.0 thresh epair &gt;= 3.2
<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> dump_modify xtcdump precision 10000 sfactor 0.1
<span class="n">dump_modify</span> <span class="mi">1</span> <span class="n">every</span> <span class="n">v_myVar</span> dump_modify 1 every 1000 nfile 20
<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> dump_modify 1 every v_myVar
</pre></div> dump_modify 1 amap min max cf 0.0 3 min green 0.5 yellow max blue boxcolor red
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <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> <em>dcd</em> style.</p>
<p>For example, the following commands will <p>For example, the following commands will
write snapshots at timesteps 0,10,20,30,100,200,300,1000,2000,etc:</p> write snapshots at timesteps 0,10,20,30,100,200,300,1000,2000,etc:</p>
<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> <pre class="literal-block">
<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> variable s equal logfreq(10,3,10)
<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> dump 1 all atom 100 tmp.dump
</pre></div> dump_modify 1 every v_s first yes
</div> </pre>
<p>The following commands would write snapshots at the timesteps listed <p>The following commands would write snapshots at the timesteps listed
in file tmp.times:</p> in file tmp.times:</p>
<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> <pre class="literal-block">
<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> variable f file tmp.times
<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> variable s equal next(f)
<span class="n">dump_modify</span> <span class="mi">1</span> <span class="n">every</span> <span class="n">v_s</span> dump 1 all atom 100 tmp.dump
</pre></div> dump_modify 1 every v_s
</div> </pre>
<div class="admonition note"> <div class="admonition note">
<p class="first admonition-title">Note</p> <p class="first admonition-title">Note</p>
<p class="last">When using a file-style variable with the <em>every</em> keyword, the <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 (large) integer, then you need to use an appropriate format. For
example, these commands:</p> example, these commands:</p>
</div> </div>
<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> <pre class="literal-block">
<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> compute 1 all property/local batom1 batom2
<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> dump 1 all local 100 tmp.bonds index c_1[1] c_1[2]
</pre></div> dump_modify 1 format &quot;%d %0.0f %0.0f&quot;
</div> </pre>
<p>will output the two atom IDs for atoms in each bond as integers. If <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 the dump_modify command were omitted, they would appear as
floating-point values, assuming they were large integers (more than 6 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 <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 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 in conjunction with the <em>type</em> argument to specify a range of atom
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 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 an asterisk with no numeric values means 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 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 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 atoms in individual molecules with a different color. See the
examples/pour/in.pour.2d.molecule input script for an example of how examples/pour/in.pour.2d.molecule input script for an example of how
this is used.</p> this is used.</p>
<div class="highlight-default"><div class="highlight"><pre><span></span>variable colors string &amp; <pre class="literal-block">
variable colors string &amp;
&quot;red green blue yellow white &amp; &quot;red green blue yellow white &amp;
purple pink orange lime gray&quot; purple pink orange lime gray&quot;
variable mol atom mol%10 variable mol atom mol%10
dump 1 all image 250 image.*.jpg v_mol type &amp; dump 1 all image 250 image.*.jpg v_mol type &amp;
zoom 1.6 adiam 1.5 zoom 1.6 adiam 1.5
dump_modify 1 pad 5 amap 0 10 sa 1 10 ${colors} dump_modify 1 pad 5 amap 0 10 sa 1 10 ${colors}
</pre></div> </pre>
</div>
<p>In this case, 10 colors are defined, and molecule IDs are <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> mapped to one of the colors, even if there are 1000s of molecules.</p>
<hr class="docutils" /> <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 <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 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 in conjunction with the <em>type</em> argument to specify a range of bond
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 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 bond types, then an asterisk with no numeric values means 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 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 trailing asterisk means all types from n to N

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@ -210,8 +210,8 @@ discussed below, it can be referenced via the following bracket
notation, where ID is the ID of the fix:</p> notation, where ID is the ID of the fix:</p>
<table border="1" class="docutils"> <table border="1" class="docutils">
<colgroup> <colgroup>
<col width="21%" /> <col width="23%" />
<col width="79%" /> <col width="77%" />
</colgroup> </colgroup>
<tbody valign="top"> <tbody valign="top">
<tr class="row-odd"><td>f_ID</td> <tr class="row-odd"><td>f_ID</td>

34
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@ -170,12 +170,12 @@
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<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">adapt</span><span class="o">/</span><span class="n">fep</span> <span class="mi">1</span> <span class="n">pair</span> <span class="n">soft</span> <span class="n">a</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">v_prefactor</span> <pre class="literal-block">
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">adapt</span><span class="o">/</span><span class="n">fep</span> <span class="mi">1</span> <span class="n">pair</span> <span class="n">soft</span> <span class="n">a</span> <span class="mi">2</span><span class="o">*</span> <span class="mi">3</span> <span class="n">v_prefactor</span> fix 1 all adapt/fep 1 pair soft a 1 1 v_prefactor
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">adapt</span><span class="o">/</span><span class="n">fep</span> <span class="mi">1</span> <span class="n">pair</span> <span class="n">lj</span><span class="o">/</span><span class="n">cut</span> <span class="n">epsilon</span> <span class="o">*</span> <span class="o">*</span> <span class="n">v_scale1</span> <span class="n">coul</span><span class="o">/</span><span class="n">cut</span> <span class="n">scale</span> <span class="mi">3</span> <span class="mi">3</span> <span class="n">v_scale2</span> <span class="n">scale</span> <span class="n">yes</span> <span class="n">reset</span> <span class="n">yes</span> fix 1 all adapt/fep 1 pair soft a 2* 3 v_prefactor
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">adapt</span><span class="o">/</span><span class="n">fep</span> <span class="mi">10</span> <span class="n">atom</span> <span class="n">diameter</span> <span class="mi">1</span> <span class="n">v_size</span> fix 1 all adapt/fep 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes
</pre></div> fix 1 all adapt/fep 10 atom diameter 1 v_size
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>
@ -307,7 +307,7 @@ each, as in the 1st example above. I &lt;= J is required. LAMMPS sets
the coefficients for the symmetric J,I interaction to the same values.</p> the coefficients for the symmetric J,I interaction to the same values.</p>
<p>A wild-card asterisk can be used in place of or in conjunction with <p>A wild-card asterisk can be used in place of or in conjunction with
the I,J arguments to set the coefficients for multiple pairs of atom the I,J arguments to set the coefficients for multiple pairs of atom
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 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 an asterisk with no numeric values means 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 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 trailing asterisk means all types from n to N
@ -333,10 +333,10 @@ details.</p>
<p>For example, these commands would change the prefactor coefficient of <p>For example, these commands would change the prefactor coefficient of
the <a class="reference internal" href="pair_soft.html"><span class="doc">pair_style soft</span></a> potential from 10.0 to 30.0 in a the <a class="reference internal" href="pair_soft.html"><span class="doc">pair_style soft</span></a> potential from 10.0 to 30.0 in a
linear fashion over the course of a simulation:</p> linear fashion over the course of a simulation:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">prefactor</span> <span class="n">equal</span> <span class="n">ramp</span><span class="p">(</span><span class="mi">10</span><span class="p">,</span><span class="mi">30</span><span class="p">)</span> <pre class="literal-block">
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">adapt</span> <span class="mi">1</span> <span class="n">pair</span> <span class="n">soft</span> <span class="n">a</span> <span class="o">*</span> <span class="o">*</span> <span class="n">v_prefactor</span> variable prefactor equal ramp(10,30)
</pre></div> fix 1 all adapt 1 pair soft a * * v_prefactor
</div> </pre>
<hr class="docutils" /> <hr class="docutils" />
<p>The <em>kspace</em> keyword used the specified variable as a scale factor on <p>The <em>kspace</em> keyword used the specified variable as a scale factor on
the energy, forces, virial calculated by whatever K-Space solver is the energy, forces, virial calculated by whatever K-Space solver is
@ -369,16 +369,14 @@ constant).</p>
<p>For example, these commands would shrink the diameter of all granular <p>For example, these commands would shrink the diameter of all granular
particles in the &#8220;center&#8221; group from 1.0 to 0.1 in a linear fashion particles in the &#8220;center&#8221; group from 1.0 to 0.1 in a linear fashion
over the course of a 1000-step simulation:</p> over the course of a 1000-step simulation:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">variable</span> <span class="n">size</span> <span class="n">equal</span> <span class="n">ramp</span><span class="p">(</span><span class="mf">1.0</span><span class="p">,</span><span class="mf">0.1</span><span class="p">)</span> <pre class="literal-block">
<span class="n">fix</span> <span class="mi">1</span> <span class="n">center</span> <span class="n">adapt</span> <span class="mi">10</span> <span class="n">atom</span> <span class="n">diameter</span> <span class="o">*</span> <span class="n">v_size</span> variable size equal ramp(1.0,0.1)
</pre></div> fix 1 center adapt 10 atom diameter * v_size
</div> </pre>
<p>For <a class="reference internal" href="run_style.html"><span class="doc">rRESPA time integration</span></a>, this fix changes <p>For <a class="reference internal" href="run_style.html"><span class="doc">rRESPA time integration</span></a>, this fix changes
parameters on the outermost rRESPA level.</p> parameters on the outermost rRESPA level.</p>
</div>
<hr class="docutils" /> <hr class="docutils" />
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info"> <p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<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 <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 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 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

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@ -140,10 +140,10 @@
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">kick</span> <span class="n">bead</span> <span class="n">addtorque</span> <span class="mf">2.0</span> <span class="mf">3.0</span> <span class="mf">5.0</span> <pre class="literal-block">
<span class="n">fix</span> <span class="n">kick</span> <span class="n">bead</span> <span class="n">addtorque</span> <span class="mf">0.0</span> <span class="mf">0.0</span> <span class="n">v_oscillate</span> fix kick bead addtorque 2.0 3.0 5.0
</pre></div> fix kick bead addtorque 0.0 0.0 v_oscillate
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>
@ -166,10 +166,8 @@ torque component.</p>
functions, and include <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command functions, and include <a class="reference internal" href="thermo_style.html"><span class="doc">thermo_style</span></a> command
keywords for the simulation box parameters and timestep and elapsed keywords for the simulation box parameters and timestep and elapsed
time. Thus it is easy to specify a time-dependent torque.</p> time. Thus it is easy to specify a time-dependent torque.</p>
</div>
<hr class="docutils" /> <hr class="docutils" />
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info"> <p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<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>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 <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 forces to the fix to add the potential &#8220;energy&#8221; inferred by the added forces to the

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@ -128,9 +128,9 @@
<span id="index-0"></span><h1>fix atc command</h1> <span id="index-0"></span><h1>fix atc command</h1>
<div class="section" id="syntax"> <div class="section" id="syntax">
<h2>Syntax</h2> <h2>Syntax</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="o">&lt;</span><span class="n">fixID</span><span class="o">&gt;</span> <span class="o">&lt;</span><span class="n">group</span><span class="o">&gt;</span> <span class="n">atc</span> <span class="o">&lt;</span><span class="nb">type</span><span class="o">&gt;</span> <span class="o">&lt;</span><span class="n">parameter_file</span><span class="o">&gt;</span> <pre class="literal-block">
</pre></div> fix &lt;fixID&gt; &lt;group&gt; atc &lt;type&gt; &lt;parameter_file&gt;
</div> </pre>
<ul class="simple"> <ul class="simple">
<li>fixID = name of fix</li> <li>fixID = name of fix</li>
<li>group = name of group fix is to be applied</li> <li>group = name of group fix is to be applied</li>
@ -148,12 +148,12 @@
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="n">AtC</span> <span class="n">internal</span> <span class="n">atc</span> <span class="n">thermal</span> <span class="n">Ar_thermal</span><span class="o">.</span><span class="n">dat</span> <pre class="literal-block">
<span class="n">fix</span> <span class="n">AtC</span> <span class="n">internal</span> <span class="n">atc</span> <span class="n">two_temperature</span> <span class="n">Ar_ttm</span><span class="o">.</span><span class="n">mat</span> fix AtC internal atc thermal Ar_thermal.dat
<span class="n">fix</span> <span class="n">AtC</span> <span class="n">internal</span> <span class="n">atc</span> <span class="n">hardy</span> fix AtC internal atc two_temperature Ar_ttm.mat
<span class="n">fix</span> <span class="n">AtC</span> <span class="n">internal</span> <span class="n">atc</span> <span class="n">field</span> fix AtC internal atc hardy
</pre></div> fix AtC internal atc field
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>
@ -163,31 +163,31 @@
<span class="c1"># ... commands to create and initialize the MD system</span> <span class="c1"># ... commands to create and initialize the MD system</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># initial fix to designate coupling type and group to apply it to</span> <pre class="literal-block">
<span class="c1"># tag group physics material_file</span> # initial fix to designate coupling type and group to apply it to
<span class="n">fix</span> <span class="n">AtC</span> <span class="n">internal</span> <span class="n">atc</span> <span class="n">thermal</span> <span class="n">Ar_thermal</span><span class="o">.</span><span class="n">mat</span> # tag group physics material_file
</pre></div> fix AtC internal atc thermal Ar_thermal.mat
</div> </pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># create a uniform 12 x 2 x 2 mesh that covers region contain the group</span> <pre class="literal-block">
<span class="c1"># nx ny nz region periodicity</span> # create a uniform 12 x 2 x 2 mesh that covers region contain the group
<span class="n">fix_modify</span> <span class="n">AtC</span> <span class="n">mesh</span> <span class="n">create</span> <span class="mi">12</span> <span class="mi">2</span> <span class="mi">2</span> <span class="n">mdRegion</span> <span class="n">f</span> <span class="n">p</span> <span class="n">p</span> # nx ny nz region periodicity
</pre></div> fix_modify AtC mesh create 12 2 2 mdRegion f p p
</div> </pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># specify the control method for the type of coupling</span> <pre class="literal-block">
<span class="c1"># physics control_type</span> # specify the control method for the type of coupling
<span class="n">fix_modify</span> <span class="n">AtC</span> <span class="n">thermal</span> <span class="n">control</span> <span class="n">flux</span> # physics control_type
</pre></div> fix_modify AtC thermal control flux
</div> </pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># specify the initial values for the empirical field &quot;temperature&quot;</span> <pre class="literal-block">
<span class="c1"># field node_group value</span> # specify the initial values for the empirical field &quot;temperature&quot;
<span class="n">fix_modify</span> <span class="n">AtC</span> <span class="n">initial</span> <span class="n">temperature</span> <span class="nb">all</span> <span class="mi">30</span> # field node_group value
</pre></div> fix_modify AtC initial temperature all 30
</div> </pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># create an output stream for nodal fields</span> <pre class="literal-block">
<span class="c1"># filename output_frequency</span> # create an output stream for nodal fields
<span class="n">fix_modify</span> <span class="n">AtC</span> <span class="n">output</span> <span class="n">atc_fe_output</span> <span class="mi">100</span> # filename output_frequency
</pre></div> fix_modify AtC output atc_fe_output 100
</div> </pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">run</span> <span class="mi">1000</span> <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">run</span> <span class="mi">1000</span>
</pre></div> </pre></div>
</div> </div>
@ -200,30 +200,30 @@
<span class="n">fix</span> <span class="n">AtC</span> <span class="n">internal</span> <span class="n">atc</span> <span class="n">hardy</span> <span class="n">fix</span> <span class="n">AtC</span> <span class="n">internal</span> <span class="n">atc</span> <span class="n">hardy</span>
</pre></div> </pre></div>
</div> </div>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># for hardy fix, specific kernel function (function type and range) to # be used as a localization function</span> <pre class="literal-block">
<span class="n">fix</span> <span class="n">AtC</span> <span class="n">kernel</span> <span class="n">quartic_sphere</span> <span class="mf">10.0</span> # for hardy fix, specific kernel function (function type and range) to # be used as a localization function
</pre></div> fix AtC kernel quartic_sphere 10.0
</div> </pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># create a uniform 1 x 1 x 1 mesh that covers region contain the group</span> <pre class="literal-block">
<span class="c1"># with periodicity this effectively creats a system average</span> # create a uniform 1 x 1 x 1 mesh that covers region contain the group
<span class="n">fix_modify</span> <span class="n">AtC</span> <span class="n">mesh</span> <span class="n">create</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="n">box</span> <span class="n">p</span> <span class="n">p</span> <span class="n">p</span> # with periodicity this effectively creats a system average
</pre></div> fix_modify AtC mesh create 1 1 1 box p p p
</div> </pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># change from default lagrangian map to eulerian</span> <pre class="literal-block">
<span class="c1"># refreshed every 100 steps</span> # change from default lagrangian map to eulerian
<span class="n">fix_modify</span> <span class="n">AtC</span> <span class="n">atom_element_map</span> <span class="n">eulerian</span> <span class="mi">100</span> # refreshed every 100 steps
</pre></div> fix_modify AtC atom_element_map eulerian 100
</div> </pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># start with no field defined</span> <pre class="literal-block">
<span class="c1"># add mass density, potential energy density, stress and temperature</span> # start with no field defined
<span class="n">fix_modify</span> <span class="n">AtC</span> <span class="n">fields</span> <span class="n">add</span> <span class="n">density</span> <span class="n">energy</span> <span class="n">stress</span> <span class="n">temperature</span> # add mass density, potential energy density, stress and temperature
</pre></div> fix_modify AtC fields add density energy stress temperature
</div> </pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># create an output stream for nodal fields</span> <pre class="literal-block">
<span class="c1"># filename output_frequency</span> # create an output stream for nodal fields
<span class="n">fix_modify</span> <span class="n">AtC</span> <span class="n">output</span> <span class="n">nvtFE</span> <span class="mi">100</span> <span class="n">text</span> # filename output_frequency
</pre></div> fix_modify AtC output nvtFE 100 text
</div> </pre>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">run</span> <span class="mi">1000</span> <div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">run</span> <span class="mi">1000</span>
</pre></div> </pre></div>
</div> </div>
@ -235,10 +235,8 @@
<p>fix_modify AtC mesh create 1 1 1 box p p p</p> <p>fix_modify AtC mesh create 1 1 1 box p p p</p>
<p>...</p> <p>...</p>
<p>Note coupling and post-processing can be combined in the same simulations using separate fixes.</p> <p>Note coupling and post-processing can be combined in the same simulations using separate fixes.</p>
</div>
<hr class="docutils" /> <hr class="docutils" />
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info"> <p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<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>. The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options relevant to this fix are listed below. 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. This fix is not invoked during <a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>.</p> <p>No information about this fix is written to <a class="reference internal" href="restart.html"><span class="doc">binary restart files</span></a>. The <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options relevant to this fix are listed below. 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. This fix is not invoked during <a class="reference internal" href="minimize.html"><span class="doc">energy minimization</span></a>.</p>
</div> </div>
<div class="section" id="restrictions"> <div class="section" id="restrictions">

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@ -156,11 +156,11 @@
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<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> <pre class="literal-block">
<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> fix 2 all atom/swap 1 1 29494 300.0 ke no types 1 2
<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> fix myFix all atom/swap 100 1 12345 298.0 region my_swap_region types 5 6
</pre></div> fix SGMC all atom/swap 1 100 345 1.0 semi-grand yes types 1 2 3 mu 0.0 4.3 -5.0
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>
@ -250,9 +250,7 @@ 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 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 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> specify if this should be done.</p>
</div> <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 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 <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 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 the <a class="reference internal" href="read_restart.html"><span class="doc">read_restart</span></a> command for info on how to

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@ -140,22 +140,22 @@
one or more input values can be listed</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[i], f_ID, f_ID[i], v_name</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> </ul>
<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> <pre class="literal-block">
<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> x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
<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> c_ID = per-atom vector calculated by a compute with ID
<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> c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
<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> f_ID = per-atom vector calculated by a fix with ID
<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> f_ID[I] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below)
</pre></div> v_name = per-atom vector calculated by an atom-style variable with name
</div> </pre>
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<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> <pre class="literal-block">
<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> fix 1 all ave/atom 1 100 100 vx vy vz
<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> fix 1 all ave/atom 10 20 1000 c_my_stress[1]
</pre></div> fix 1 all ave/atom 10 20 1000 c_my_stress[*]
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <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> per-atom vectors.</p>
<p>Note that for values from a compute or fix, the bracketed index I can <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 be specified using a wildcard asterisk with the index to effectively
specify multiple values. This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or 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 size of the vector (for <em>mode</em> = scalar) or the &#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 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 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 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> 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> command creates a per-atom array with 6 columns:</p>
<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> <pre class="literal-block">
<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> compute my_stress all stress/atom NULL
<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> fix 1 all ave/atom 10 20 1000 c_my_stress[*]
<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> fix 1 all ave/atom 10 20 1000 c_my_stress[1] c_my_stress[1] &amp;
<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> c_my_stress[3] c_my_stress[4] &amp;
</pre></div> c_my_stress[5] c_my_stress[6]
</div> </pre>
<hr class="docutils" /> <hr class="docutils" />
<p>The <em>Nevery</em>, <em>Nrepeat</em>, and <em>Nfreq</em> arguments specify on what <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 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 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> attributes.</p>
</div> </div>
<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 <p>If a value begins with &#8220;c_&#8221;, a compute ID must follow which has been
previously defined in the input script. If no bracketed term is previously defined in the input script. If no bracketed term is
appended, the per-atom vector calculated by the compute is used. If a 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 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 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 be specified with a wildcard asterisk to effectively specify multiple
values.</p> values.</p>
<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 <p>If a value begins with &#8220;f_&#8221;, a fix ID must follow which has been
previously defined in the input script. If no bracketed term is previously defined in the input script. If no bracketed term is
appended, the per-atom vector calculated by the fix is used. If a 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 bracketed term containing an index I is appended, the Ith column of
@ -246,15 +246,13 @@ 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 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 be specified with a wildcard asterisk to effectively specify multiple
values.</p> values.</p>
<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 <p>If a value begins with &#8220;v_&#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 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 thermodynamic keywords, or invoke other computes, fixes, or variables
when they are evaluated, so this is a very general means of generating when they are evaluated, so this is a very general means of generating
per-atom quantities to time average.</p> per-atom quantities to time average.</p>
</div>
<hr class="docutils" /> <hr class="docutils" />
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info"> <p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<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 <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 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> 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>

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@ -141,16 +141,16 @@
<li>one or more input values can be listed</li> <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> <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> </ul>
<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> <pre class="literal-block">
<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> vx,vy,vz,fx,fy,fz = atom attribute (velocity, force component)
<span class="n">temp</span> <span class="o">=</span> <span class="n">temperature</span> density/number, density/mass = number or mass density
<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> temp = temperature
<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> c_ID = per-atom vector calculated by a compute with ID
<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> c_ID[I] = Ith column of per-atom array calculated by a compute with ID, I can include wildcard (see below)
<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> f_ID = per-atom vector calculated by a fix with ID
<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> f_ID[I] = Ith column of per-atom array calculated by a fix with ID, I can include wildcard (see below)
</pre></div> v_name = per-atom vector calculated by an atom-style variable with name
</div> </pre>
<ul class="simple"> <ul class="simple">
<li>zero or more keyword/arg pairs may be appended</li> <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> <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 @@
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<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> <pre class="literal-block">
<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> fix 1 all ave/chunk 10000 1 10000 binchunk c_myCentro title1 &quot;My output values&quot;
<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> fix 1 flow ave/chunk 100 10 1000 molchunk vx vz norm sample file vel.profile
<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> fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running
</pre></div> fix 1 flow ave/chunk 100 5 1000 binchunk density/mass ave running
</div> </pre>
<p><strong>NOTE:</strong></p> <p><strong>NOTE:</strong></p>
<p>If you are trying to replace a deprectated fix ave/spatial command <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 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> produce global quantities.</p>
<p>Note that for values from a compute or fix, the bracketed index I can <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 be specified using a wildcard asterisk with the index to effectively
specify multiple values. This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or 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 size of the vector (for <em>mode</em> = scalar) or the &#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 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 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 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 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> case, a per-atom array with 3 columns:</p>
<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> <pre class="literal-block">
<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> compute myAng all property/atom angmomx angmomy angmomz
<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> fix 1 all ave/chunk 100 1 100 cc1 c_myAng[*] file tmp.angmom
</pre></div> fix 2 all ave/chunk 100 1 100 cc1 c_myAng[1] c_myAng[2] c_myAng[3] file tmp.angmom
</div> </pre>
<div class="admonition note"> <div class="admonition note">
<p class="first admonition-title">Note</p> <p class="first admonition-title">Note</p>
<p class="last">This fix works by creating an array of size <em>Nchunk</em> by Nvalues <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 of atoms to calculate their temperature. The compute allows the
center-of-mass velocity of each chunk to be subtracted before center-of-mass velocity of each chunk to be subtracted before
calculating the temperature; this fix does not.</p> calculating the temperature; this fix does not.</p>
<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 <p>If a value begins with &#8220;c_&#8221;, a compute ID must follow which has been
previously defined in the input script. If no bracketed integer is previously defined in the input script. If no bracketed integer is
appended, the per-atom vector calculated by the compute is used. If a 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 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>. 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 See the discussion above for how I can be specified with a wildcard
asterisk to effectively specify multiple values.</p> asterisk to effectively specify multiple values.</p>
<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 <p>If a value begins with &#8220;f_&#8221;, a fix ID must follow which has been
previously defined in the input script. If no bracketed integer is previously defined in the input script. If no bracketed integer is
appended, the per-atom vector calculated by the fix is used. If a 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 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 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 discussion above for how I can be specified with a wildcard asterisk
to effectively specify multiple values.</p> to effectively specify multiple values.</p>
<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 <p>If a value begins with &#8220;v_&#8221;, a variable name must follow which has
been previously defined in the input script. Variables of style been previously defined in the input script. Variables of style
<em>atom</em> can reference thermodynamic keywords and various per-atom <em>atom</em> can reference thermodynamic keywords and various per-atom
attributes, or invoke other computes, fixes, or variables when they attributes, or invoke other computes, fixes, or variables when they
@ -502,10 +502,8 @@ 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 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 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> 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" /> <hr class="docutils" />
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info"> <p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<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 <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> are relevant to this fix.</p>
<p>This fix computes a global array of values which can be accessed by <p>This fix computes a global array of values which can be accessed by

82
doc/html/fix_ave_correlate.html
View File

@ -140,14 +140,14 @@
<li>one or more input values can be listed</li> <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> <li>value = c_ID, c_ID[N], f_ID, f_ID[N], v_name</li>
</ul> </ul>
<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> <pre class="literal-block">
<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="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> c_ID = global scalar calculated by a compute with ID
<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> c_ID[I] = Ith component of global vector calculated by a compute with ID, I can include wildcard (see below)
<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="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> f_ID = global scalar calculated by a fix with ID
<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> f_ID[I] = Ith component of global vector calculated by a fix with ID, I can include wildcard (see below)
<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">Ith</span> <span class="n">component</span> <span class="n">of</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> v_name = global value calculated by an equal-style variable with name
</pre></div> v_name[I] = Ith component of a vector-style variable with name
</div> </pre>
<ul class="simple"> <ul class="simple">
<li>zero or more keyword/arg pairs may be appended</li> <li>zero or more keyword/arg pairs may be appended</li>
<li>keyword = <em>type</em> or <em>ave</em> or <em>start</em> or <em>prefactor</em> or <em>file</em> or <em>overwrite</em> or <em>title1</em> or <em>title2</em> or <em>title3</em></li> <li>keyword = <em>type</em> or <em>ave</em> or <em>start</em> or <em>prefactor</em> or <em>file</em> or <em>overwrite</em> or <em>title1</em> or <em>title2</em> or <em>title3</em></li>
@ -180,12 +180,12 @@
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<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="mi">5</span> <span class="mi">100</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> <pre class="literal-block">
<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="mi">1</span> <span class="mi">50</span> <span class="mi">10000</span> <span class="o">&amp;</span> fix 1 all ave/correlate 5 100 1000 c_myTemp file temp.correlate
<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> fix 1 all ave/correlate 1 50 10000 &amp;
<span class="nb">type</span> <span class="n">upper</span> <span class="n">ave</span> <span class="n">running</span> <span class="n">title1</span> <span class="s2">&quot;My correlation data&quot;</span> c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &amp;
</pre></div> type upper ave running title1 &quot;My correlation data&quot;
</div> </pre>
<p>fix 1 all ave/correlate 1 50 10000 c_thermo_press[*]</p> <p>fix 1 all ave/correlate 1 50 10000 c_thermo_press[*]</p>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
@ -221,7 +221,7 @@ ones that can be used with this fix. Variables of style <em>atom</em> cannot
be used, since they produce per-atom values.</p> be used, since they produce per-atom values.</p>
<p>Note that for values from a compute or fix, the bracketed index I can <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 be specified using a wildcard asterisk with the index to effectively
specify multiple values. This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or 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 size of the vector (for <em>mode</em> = scalar) or the &#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 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 with no numeric values means all indices from 1 to N. A leading
@ -232,13 +232,13 @@ means all indices from m to n (inclusive).</p>
vector had been listed one by one. E.g. these 2 fix ave/correlate vector had been listed one by one. E.g. these 2 fix ave/correlate
commands are equivalent, since the <a class="reference internal" href="compute_pressure.html"><span class="doc">compute pressure</span></a> command creates a global vector with 6 commands are equivalent, since the <a class="reference internal" href="compute_pressure.html"><span class="doc">compute pressure</span></a> command creates a global vector with 6
values.</p> values.</p>
<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">pressure</span> <span class="n">NULL</span> <pre class="literal-block">
<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="mi">1</span> <span class="mi">50</span> <span class="mi">10000</span> <span class="n">c_myPress</span><span class="p">[</span><span class="o">*</span><span class="p">]</span> compute myPress all pressure NULL
<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="mi">1</span> <span class="mi">50</span> <span class="mi">10000</span> <span class="o">&amp;</span> fix 1 all ave/correlate 1 50 10000 c_myPress[*]
<span class="n">c_myPress</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="n">c_myPress</span><span class="p">[</span><span class="mi">2</span><span class="p">]</span> <span class="n">c_myPress</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span> <span class="o">&amp;</span> fix 1 all ave/correlate 1 50 10000 &amp;
<span class="n">c_myPress</span><span class="p">[</span><span class="mi">4</span><span class="p">]</span> <span class="n">c_myPress</span><span class="p">[</span><span class="mi">5</span><span class="p">]</span> <span class="n">c_myPress</span><span class="p">[</span><span class="mi">6</span><span class="p">]</span> c_myPress[1] c_myPress[2] c_myPress[3] &amp;
</pre></div> c_myPress[4] c_myPress[5] c_myPress[6]
</div> </pre>
<hr class="docutils" /> <hr class="docutils" />
<p>The <em>Nevery</em>, <em>Nrepeat</em>, and <em>Nfreq</em> arguments specify on what <p>The <em>Nevery</em>, <em>Nrepeat</em>, and <em>Nfreq</em> arguments specify on what
timesteps the input values will be used to calculate correlation data. timesteps the input values will be used to calculate correlation data.
@ -249,9 +249,9 @@ initial time up to an output timestep. The initial time could be the
beginning of the simulation or the last output time; see the <em>ave</em> beginning of the simulation or the last output time; see the <em>ave</em>
keyword for options. For the set of samples, the correlation value keyword for options. For the set of samples, the correlation value
Cij is calculated as:</p> Cij is calculated as:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Cij</span><span class="p">(</span><span class="n">delta</span><span class="p">)</span> <span class="o">=</span> <span class="n">ave</span><span class="p">(</span><span class="n">Vi</span><span class="p">(</span><span class="n">t</span><span class="p">)</span><span class="o">*</span><span class="n">Vj</span><span class="p">(</span><span class="n">t</span><span class="o">+</span><span class="n">delta</span><span class="p">))</span> <pre class="literal-block">
</pre></div> Cij(delta) = ave(Vi(t)*Vj(t+delta))
</div> </pre>
<p>which is the correlation value between input values Vi and Vj, <p>which is the correlation value between input values Vi and Vj,
separated by time delta. Note that the second value Vj in the pair is separated by time delta. Note that the second value Vj in the pair is
always the one sampled at the later time. The ave() represents an always the one sampled at the later time. The ave() represents an
@ -259,9 +259,9 @@ average over every pair of samples in the set that are separated by
time delta. The maximum delta used is of size (<em>Nrepeat</em>-1)*<em>Nevery</em>. time delta. The maximum delta used is of size (<em>Nrepeat</em>-1)*<em>Nevery</em>.
Thus the correlation between a pair of input values yields <em>Nrepeat</em> Thus the correlation between a pair of input values yields <em>Nrepeat</em>
correlation datums:</p> correlation datums:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Cij</span><span class="p">(</span><span class="mi">0</span><span class="p">),</span> <span class="n">Cij</span><span class="p">(</span><span class="n">Nevery</span><span class="p">),</span> <span class="n">Cij</span><span class="p">(</span><span class="mi">2</span><span class="o">*</span><span class="n">Nevery</span><span class="p">),</span> <span class="o">...</span><span class="p">,</span> <span class="n">Cij</span><span class="p">((</span><span class="n">Nrepeat</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span><span class="o">*</span><span class="n">Nevery</span><span class="p">)</span> <pre class="literal-block">
</pre></div> Cij(0), Cij(Nevery), Cij(2*Nevery), ..., Cij((Nrepeat-1)*Nevery)
</div> </pre>
<p>For example, if Nevery=5, Nrepeat=6, and Nfreq=100, then values on <p>For example, if Nevery=5, Nrepeat=6, and Nfreq=100, then values on
timesteps 0,5,10,15,...,100 will be used to compute the final averages timesteps 0,5,10,15,...,100 will be used to compute the final averages
on timestep 100. Six averages will be computed: Cij(0), Cij(5), on timestep 100. Six averages will be computed: Cij(0), Cij(5),
@ -272,7 +272,7 @@ Vi(10)*V j20), Vi(15)*Vj(25), ..., Vi(85)*Vj(95), Vi(90)*Vj(100).</p>
non-zero. Also, if the <em>ave</em> keyword is set to <em>one</em> which is the non-zero. Also, if the <em>ave</em> keyword is set to <em>one</em> which is the
default, then <em>Nfreq</em> &gt;= (<em>Nrepeat</em>-1)*<em>Nevery</em> is required.</p> default, then <em>Nfreq</em> &gt;= (<em>Nrepeat</em>-1)*<em>Nevery</em> is required.</p>
<hr class="docutils" /> <hr class="docutils" />
<p>If a value begins with &#8220;<a href="#id3"><span class="problematic" id="id4">c_</span></a>&#8221;, a compute ID must follow which has been <p>If a value begins with &#8220;c_&#8221;, a compute ID must follow which has been
previously defined in the input script. If no bracketed term is previously defined in the input script. If no bracketed term is
appended, the global scalar calculated by the compute is used. If a appended, the global scalar calculated by the compute is used. If a
bracketed term is appended, the Ith element of the global vector bracketed term is appended, the Ith element of the global vector
@ -286,7 +286,7 @@ defined not in your input script, but by <a class="reference internal" href="the
or <a class="reference internal" href="fix_temp_rescale.html"><span class="doc">fix temp/rescale</span></a>. See the doc pages for 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 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> 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;<a href="#id5"><span class="problematic" id="id6">f_</span></a>&#8221;, a fix ID must follow which has been <p>If a value begins with &#8220;f_&#8221;, a fix ID must follow which has been
previously defined in the input script. If no bracketed term is previously defined in the input script. If no bracketed term is
appended, the global scalar calculated by the fix is used. If a appended, the global scalar calculated by the fix is used. If a
bracketed term is appended, the Ith element of the global vector bracketed term is appended, the Ith element of the global vector
@ -296,7 +296,7 @@ values.</p>
<p>Note that some fixes only produce their values on certain timesteps, <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. 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> 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;<a href="#id7"><span class="problematic" id="id8">v_</span></a>&#8221;, a variable name must follow which has <p>If a value begins with &#8220;v_&#8221;, a variable name must follow which has
been previously defined in the input script. Only equal-style or been previously defined in the input script. Only equal-style or
vector-style variables can be referenced; the latter requires a vector-style variables can be referenced; the latter requires a
bracketed term to specify the Ith element of the vector calculated by bracketed term to specify the Ith element of the vector calculated by
@ -366,11 +366,11 @@ the strings that will be printed as the first 3 lines of the output
file, assuming the <em>file</em> keyword was used. LAMMPS uses default file, assuming the <em>file</em> keyword was used. LAMMPS uses default
values for each of these, so they do not need to be specified.</p> values for each of these, so they do not need to be specified.</p>
<p>By default, these header lines are as follows:</p> <p>By default, these header lines are as follows:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="c1"># Time-correlated data for fix ID</span> <pre class="literal-block">
<span class="c1"># TimeStep Number-of-time-windows</span> # Time-correlated data for fix ID
<span class="c1"># Index TimeDelta Ncount valueI*valueJ valueI*valueJ ...</span> # TimeStep Number-of-time-windows
</pre></div> # Index TimeDelta Ncount valueI*valueJ valueI*valueJ ...
</div> </pre>
<p>In the first line, ID is replaced with the fix-ID. The second line <p>In the first line, ID is replaced with the fix-ID. The second line
describes the two values that are printed at the first of each section describes the two values that are printed at the first of each section
of output. In the third line the value pairs are replaced with the of output. In the third line the value pairs are replaced with the
@ -378,9 +378,9 @@ appropriate fields from the fix ave/correlate command.</p>
<hr class="docutils" /> <hr class="docutils" />
<p>Let Sij = a set of time correlation data for input values I and J, <p>Let Sij = a set of time correlation data for input values I and J,
namely the <em>Nrepeat</em> values:</p> namely the <em>Nrepeat</em> values:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Sij</span> <span class="o">=</span> <span class="n">Cij</span><span class="p">(</span><span class="mi">0</span><span class="p">),</span> <span class="n">Cij</span><span class="p">(</span><span class="n">Nevery</span><span class="p">),</span> <span class="n">Cij</span><span class="p">(</span><span class="mi">2</span><span class="o">*</span><span class="n">Nevery</span><span class="p">),</span> <span class="o">...</span><span class="p">,</span> <span class="n">Cij</span><span class="p">(</span><span class="o">*</span><span class="n">Nrepeat</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span><span class="o">*</span><span class="n">Nevery</span><span class="p">)</span> <pre class="literal-block">
</pre></div> Sij = Cij(0), Cij(Nevery), Cij(2*Nevery), ..., Cij(*Nrepeat-1)*Nevery)
</div> </pre>
<p>As explained below, these datums are output as one column of a global <p>As explained below, these datums are output as one column of a global
array, which is effectively the correlation matrix.</p> array, which is effectively the correlation matrix.</p>
<p>The <em>trap</em> function defined for <a class="reference internal" href="variable.html"><span class="doc">equal-style variables</span></a> <p>The <em>trap</em> function defined for <a class="reference internal" href="variable.html"><span class="doc">equal-style variables</span></a>
@ -389,10 +389,8 @@ using a trapezoidal rule. This is useful for calculating various
quantities which can be derived from time correlation data. If a quantities which can be derived from time correlation data. If a
normalization factor is needed for the time integration, it can be normalization factor is needed for the time integration, it can be
included in the variable formula or via the <em>prefactor</em> keyword.</p> included in the variable formula or via the <em>prefactor</em> keyword.</p>
</div>
<hr class="docutils" /> <hr class="docutils" />
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info"> <p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<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 <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> are relevant to this fix.</p>
<p>This fix computes a global array of values which can be accessed by <p>This fix computes a global array of values which can be accessed by

30
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View File

@ -139,13 +139,13 @@
<li>one or more input values can be listed</li> <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> <li>value = c_ID, c_ID[N], f_ID, f_ID[N], v_name</li>
</ul> </ul>
<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> <pre class="literal-block">
<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> c_ID = global scalar calculated by a compute with ID
<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> c_ID[I] = Ith component of global vector calculated by a compute with ID
<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> f_ID = global scalar calculated by a fix with ID
<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> f_ID[I] = Ith component of global vector calculated by a fix with ID
</pre></div> v_name = global value calculated by an equal-style variable with name
</div> </pre>
<ul class="simple"> <ul class="simple">
<li>zero or more keyword/arg pairs may be appended</li> <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> <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 @@
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<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> <pre class="literal-block">
<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> fix 1 all ave/correlate/long 5 1000 c_myTemp file temp.correlate
<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> fix 1 all ave/correlate/long 1 10000 &amp;
<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> c_thermo_press[1] c_thermo_press[2] c_thermo_press[3] &amp;
</pre></div> type upper title1 &quot;My correlation data&quot; nlen 15 ncount 3
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>
@ -221,9 +221,7 @@ steps can be calculated.</p>
4*ncorr*nlen*8 bytes. With the default values of the parameters, this 4*ncorr*nlen*8 bytes. With the default values of the parameters, this
corresponds to about 10 KB.</p> 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>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>
</div> <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>Since this fix in intended for the calculation of time correlation <p>Since this fix in intended for the calculation of time correlation
functions over very long MD simulations, the information about this functions over very long MD simulations, the information about this
fix is written automatically to binary restart files, so that the time 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>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> <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> </ul>
<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> <pre class="literal-block">
<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> x,y,z,vx,vy,vz,fx,fy,fz = atom attribute (position, velocity, force component)
<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> c_ID = scalar or vector calculated by a compute with ID
<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> c_ID[I] = Ith component of vector or Ith column of array calculated by a compute with ID, I can include wildcard (see below)
<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> f_ID = scalar or vector calculated by a fix with ID
<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> f_ID[I] = Ith component of vector or Ith column of array calculated by a fix with ID, I can include wildcard (see below)
<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> v_name = value(s) calculated by an equal-style or vector-style or atom-style variable with name
</pre></div> v_name[I] = value calculated by a vector-style variable with name
</div> </pre>
<ul class="simple"> <ul class="simple">
<li>zero or more keyword/arg pairs may be appended</li> <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> <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 @@
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<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> <pre class="literal-block">
<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> fix 1 all ave/histo 100 5 1000 0.5 1.5 50 c_myTemp file temp.histo ave running
<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> 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;
<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> fix 1 all ave/histo 100 5 1000 -5 5 100 c_thermo_press[*]
<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> fix 1 all ave/histo 1 100 1000 -2.0 2.0 18 vx vy vz mode vector ave running beyond extra
</pre></div> fix 1 all ave/histo/weight 1 1 1 10 100 2000 c_XRD[1] c_XRD[2]
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <h2>Description</h2>
@ -232,7 +232,7 @@ with a bracketed term appended, indicating the Ith column of the array
is used.</p> is used.</p>
<p>Note that for values from a compute or fix, the bracketed index I can <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 be specified using a wildcard asterisk with the index to effectively
specify multiple values. This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or 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 size of the vector (for <em>mode</em> = scalar) or the &#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 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 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 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 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> 3 columns:</p>
<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> <pre class="literal-block">
<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> compute myCOM all com/chunk
<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> fix 1 all ave/histo 100 1 100 c_myCOM[*] file tmp1.com mode vector
</pre></div> fix 2 all ave/histo 100 1 100 c_myCOM[1] c_myCOM[2] c_myCOM[3] file tmp2.com mode vector
</div> </pre>
<p>If the fix ave/histo/weight command is used, exactly two values must <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 be specified. If the values are vectors, they must be the same
length. The first value (a scalar or vector) is what is histogrammed 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 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 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> an input value from that compute.</p>
<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 <p>If a value begins with &#8220;c_&#8221;, a compute ID must follow which has been
previously defined in the input script. If <em>mode</em> = scalar, then if previously defined in the input script. If <em>mode</em> = scalar, then if
no bracketed term is appended, the global scalar calculated by the no bracketed term is appended, the global scalar calculated by the
compute is used. If a bracketed term is appended, the Ith element of 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 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. 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> 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;<a href="#id3"><span class="problematic" id="id4">f_</span></a>&#8221;, a fix ID must follow which has been <p>If a value begins with &#8220;f_&#8221;, a fix ID must follow which has been
previously defined in the input script. If <em>mode</em> = scalar, then if 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 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 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, <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. 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> 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;<a href="#id5"><span class="problematic" id="id6">v_</span></a>&#8221;, a variable name must follow which has <p>If a value begins with &#8220;v_&#8221;, a variable name must follow which has
been previously defined in the input script. If <em>mode</em> = scalar, then 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 only equal-style or vector-style variables can be used, which both
produce global values. In this mode, a vector-style variable requires produce global values. In this mode, a vector-style variable requires
@ -399,10 +399,8 @@ 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 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 of output. The third describes the 4 values printed for each bin in
the histogram.</p> the histogram.</p>
</div>
<hr class="docutils" /> <hr class="docutils" />
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info"> <p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<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 <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> are relevant to this fix.</p>
<p>This fix produces a global vector and global array which can be <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>one or more input values can be listed</li>
<li>value = c_ID, c_ID[N], f_ID, f_ID[N], v_name</li> <li>value = c_ID, c_ID[N], f_ID, f_ID[N], v_name</li>
</ul> </ul>
<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> <pre class="literal-block">
<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> c_ID = global scalar or vector calculated by a compute with ID
<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> 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)
<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> f_ID = global scalar or vector calculated by a fix with ID
<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> 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)
<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> v_name = value(s) calculated by an equal-style or vector-style variable with name
</pre></div> v_name[I] = value calculated by a vector-style variable with name
</div> </pre>
<ul class="simple"> <ul class="simple">
<li>zero or more keyword/arg pairs may be appended</li> <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> <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 @@
</div> </div>
<div class="section" id="examples"> <div class="section" id="examples">
<h2>Examples</h2> <h2>Examples</h2>
<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> <pre class="literal-block">
<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> fix 1 all ave/time 100 5 1000 c_myTemp c_thermo_temp file temp.profile
<span class="n">title1</span> <span class="s2">&quot;My output values&quot;</span> fix 1 all ave/time 100 5 1000 c_thermo_press[2] ave window 20 &amp;
<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> title1 &quot;My output values&quot;
<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> fix 1 all ave/time 100 5 1000 c_thermo_press[*]
</pre></div> fix 1 all ave/time 1 100 1000 f_indent f_indent[1] file temp.indent off 1
</div> </pre>
</div> </div>
<div class="section" id="description"> <div class="section" id="description">
<h2>Description</h2> <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> 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 <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 be specified using a wildcard asterisk with the index to effectively
specify multiple values. This takes the form &#8220;*&#8221; or &#8220;<em>n&#8221; or &#8220;n</em>&#8221; or 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 size of the vector (for <em>mode</em> = scalar) or the &#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 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 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 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 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> with 3 columns, each of length 50:</p>
<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> <pre class="literal-block">
<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> compute myRDF all rdf 50 1 2
<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> fix 1 all ave/time 100 1 100 c_myRDF[*] file tmp1.rdf mode vector
</pre></div> fix 2 all ave/time 100 1 100 c_myRDF[1] c_myRDF[2] c_myRDF[3] file tmp2.rdf mode vector
</div> </pre>
<hr class="docutils" /> <hr class="docutils" />
<p>The <em>Nevery</em>, <em>Nrepeat</em>, and <em>Nfreq</em> arguments specify on what <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 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 averaging is done; values are simply generated on timesteps
100,200,etc.</p> 100,200,etc.</p>
<hr class="docutils" /> <hr class="docutils" />
<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 <p>If a value begins with &#8220;c_&#8221;, a compute ID must follow which has been
previously defined in the input script. If <em>mode</em> = scalar, then if previously defined in the input script. If <em>mode</em> = scalar, then if
no bracketed term is appended, the global scalar calculated by the no bracketed term is appended, the global scalar calculated by the
compute is used. If a bracketed term is appended, the Ith element of 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 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. 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> 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;<a href="#id3"><span class="problematic" id="id4">f_</span></a>&#8221;, a fix ID must follow which has been <p>If a value begins with &#8220;f_&#8221;, a fix ID must follow which has been
previously defined in the input script. If <em>mode</em> = scalar, then if 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 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 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, <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. 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> 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;<a href="#id5"><span class="problematic" id="id6">v_</span></a>&#8221;, a variable name must follow which has <p>If a value begins with &#8220;v_&#8221;, a variable name must follow which has
been previously defined in the input script. If <em>mode</em> = scalar, then 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 only equal-style or vector-style variables can be used, which both
produce global values. In this mode, a vector-style variable requires produce global values. In this mode, a vector-style variable requires
@ -383,10 +383,8 @@ 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 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 of output. In the third line the values are replaced with the
appropriate fields from the fix ave/time command.</p> appropriate fields from the fix ave/time command.</p>
</div>
<hr class="docutils" /> <hr class="docutils" />
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info"> <p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<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 <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> are relevant to this fix.</p>
<p>This fix produces a global scalar or global vector or global array <p>This fix produces a global scalar or global vector or global array

4
doc/html/fix_balance.html
View File

@ -432,10 +432,8 @@ will be duplicate nodes in the list.</p>
rectangle for each processor (1 to 4).</p> rectangle for each processor (1 to 4).</p>
<p>For a 3d problem, the syntax is similar with 8 vertices listed for <p>For a 3d problem, the syntax is similar with 8 vertices listed for
each processor, instead of 4, and &#8220;SQUARES&#8221; replaced by &#8220;CUBES&#8221;.</p> each processor, instead of 4, and &#8220;SQUARES&#8221; replaced by &#8220;CUBES&#8221;.</p>
</div>
<hr class="docutils" /> <hr class="docutils" />
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info"> <p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<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 <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> are relevant to this fix.</p>
<p>This fix computes a global scalar which is the imbalance factor <p>This fix computes a global scalar which is the imbalance factor

4
doc/html/fix_bond_break.html
View File

@ -224,10 +224,8 @@ dramatically released when the bond is broken. More generally, you
may need to thermostat your system to compensate for energy changes may need to thermostat your system to compensate for energy changes
resulting from broken bonds (and angles, dihedrals, impropers).</p> resulting from broken bonds (and angles, dihedrals, impropers).</p>
</div> </div>
</div>
<hr class="docutils" /> <hr class="docutils" />
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info"> <p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<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 <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> are relevant to this fix.</p>
<p>This fix computes two statistics which it stores in a global vector of <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 1st, 2nd, and 3rd neighbors of each atom (within the bond topology of
the system) for use in weighting pairwise interactions for bonded the system) for use in weighting pairwise interactions for bonded
atoms. Note that adding a single bond always adds a new 1st neighbor atoms. Note that adding a single bond always adds a new 1st neighbor
but may also induce <em>many</em> new 2nd and 3rd neighbors, depending on the but may also induce *many* new 2nd and 3rd neighbors, depending on the
molecular topology of your system. The &#8220;extra special per atom&#8221; molecular topology of your system. The &#8220;extra special per atom&#8221;
parameter must typically be set to allow for the new maximum total 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 size (1st + 2nd + 3rd neighbors) of this per-atom list. There are 3
@ -320,10 +320,8 @@ dramatically when the bond is formed. More generally, you may need to
thermostat your system to compensate for energy changes resulting from thermostat your system to compensate for energy changes resulting from
created bonds (and angles, dihedrals, impropers).</p> created bonds (and angles, dihedrals, impropers).</p>
</div> </div>
</div>
<hr class="docutils" /> <hr class="docutils" />
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info"> <p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></p>
<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 <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> are relevant to this fix.</p>
<p>This fix computes two statistics which it stores in a global vector of <p>This fix computes two statistics which it stores in a global vector of

6
doc/html/fix_bond_swap.html
View File

@ -229,9 +229,9 @@ quantities or the printing of unwrapped coordinates to a dump file.</p>
<p>This fix computes a temperature each time it is invoked for use by the <p>This fix computes a temperature each time it is invoked for use by the
Boltzmann criterion. To do this, the fix creates its own compute of Boltzmann criterion. To do this, the fix creates its own compute of
style <em>temp</em>, as if this command had been issued:</p> style <em>temp</em>, as if this command had been issued:</p>
<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> <pre class="literal-block">
</pre></div> compute fix-ID_temp all temp
</div> </pre>
<p>See the <a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a> command for details. Note <p>See the <a class="reference internal" href="compute_temp.html"><span class="doc">compute temp</span></a> command for details. Note
that the ID of the new compute is the fix-ID with underscore + &#8220;temp&#8221; that the ID of the new compute is the fix-ID with underscore + &#8220;temp&#8221;
appended and the group for the new compute is &#8220;all&#8221;, so that the appended and the group for the new compute is &#8220;all&#8221;, so that the

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