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update docs for lj/sf/dipole/sf

This commit is contained in:
Axel Kohlmeyer 2016-09-09 10:00:15 -04:00
parent 37833b537b
commit d70e051ecd
5 changed files with 50 additions and 39 deletions
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24
doc/html/compute_rdf.html
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@ -141,13 +141,13 @@
</div>
<div class="section" id="examples">
<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">rdf</span> <span class="mi">100</span>
<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">rdf</span> <span class="mi">100</span> <span class="mi">1</span> <span class="mi">1</span>
<span class="n">compute</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">rdf</span> <span class="mi">100</span> <span class="o">*</span> <span class="mi">3</span>
<span class="n">compute</span> <span class="mi">1</span> <span class="n">fluid</span> <span class="n">rdf</span> <span class="mi">500</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">2</span> <span class="mi">1</span> <span class="mi">2</span> <span class="mi">2</span>
<span class="n">compute</span> <span class="mi">1</span> <span class="n">fluid</span> <span class="n">rdf</span> <span class="mi">500</span> <span class="mi">1</span><span class="o">*</span><span class="mi">3</span> <span class="mi">2</span> <span class="mi">5</span> <span class="o">*</span><span class="mi">10</span>
</pre></div>
</div>
<pre class="literal-block">
compute 1 all rdf 100
compute 1 all rdf 100 1 1
compute 1 all rdf 100 * 3
compute 1 fluid rdf 500 1 1 1 2 2 1 2 2
compute 1 fluid rdf 500 1*3 2 5 *10
</pre>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -184,7 +184,7 @@ listed, then a separate histogram is generated for each
<p>The <em>itypeN</em> and <em>jtypeN</em> settings can be specified in one of two
ways. An explicit numeric value can be used, as in the 4th example
above. Or a wild-card asterisk can be used 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
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
@ -226,10 +226,10 @@ atoms of type jtypeN.</p>
<p>The simplest way to output the results of the compute rdf 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>
<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="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">tmp</span><span class="o">.</span><span class="n">rdf</span> <span class="n">mode</span> <span class="n">vector</span>
</pre></div>
</div>
<pre class="literal-block">
compute myRDF all rdf 50
fix 1 all ave/time 100 1 100 c_myRDF[*] file tmp.rdf mode vector
</pre>
<p><strong>Output info:</strong></p>
<p>This compute calculates a global array with the number of rows =
<em>Nbins</em>, and the number of columns = 1 + 2*Npairs, where Npairs is the

52
doc/html/fix_adapt.html
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@ -165,12 +165,12 @@
</div>
<div class="section" id="examples">
<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="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>
<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="mi">2</span><span class="o">*</span> <span class="mi">3</span> <span class="n">v_prefactor</span>
<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">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>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">adapt</span> <span class="mi">10</span> <span class="n">atom</span> <span class="n">diameter</span> <span class="n">v_size</span>
</pre></div>
</div>
<pre class="literal-block">
fix 1 all adapt 1 pair soft a 1 1 v_prefactor
fix 1 all adapt 1 pair soft a 2* 3 v_prefactor
fix 1 all adapt 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes
fix 1 all adapt 10 atom diameter v_size
</pre>
</div>
<div class="section" id="description">
<h2>Description</h2>
@ -225,8 +225,8 @@ meaning of these parameters:</p>
<table border="1" class="docutils">
<colgroup>
<col width="49%" />
<col width="35%" />
<col width="17%" />
<col width="36%" />
<col width="15%" />
</colgroup>
<tbody valign="top">
<tr class="row-odd"><td><a class="reference internal" href="pair_born.html"><span class="doc">born</span></a></td>
@ -257,23 +257,27 @@ meaning of these parameters:</p>
<td>epsilon,sigma,delta</td>
<td>type pairs</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_lubricate.html"><span class="doc">lubricate</span></a></td>
<tr class="row-even"><td><a class="reference internal" href="pair_dipole.html"><span class="doc">lj/sf/dipole/sf</span></a></td>
<td>epsilon,sigma,scale</td>
<td>type pairs</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_lubricate.html"><span class="doc">lubricate</span></a></td>
<td>mu</td>
<td>global</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_gauss.html"><span class="doc">gauss</span></a></td>
<tr class="row-even"><td><a class="reference internal" href="pair_gauss.html"><span class="doc">gauss</span></a></td>
<td>a</td>
<td>type pairs</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_morse.html"><span class="doc">morse</span></a></td>
<tr class="row-odd"><td><a class="reference internal" href="pair_morse.html"><span class="doc">morse</span></a></td>
<td>d0,r0,alpha</td>
<td>type pairs</td>
</tr>
<tr class="row-odd"><td><a class="reference internal" href="pair_soft.html"><span class="doc">soft</span></a></td>
<tr class="row-even"><td><a class="reference internal" href="pair_soft.html"><span class="doc">soft</span></a></td>
<td>a</td>
<td>type pairs</td>
</tr>
<tr class="row-even"><td><a class="reference internal" href="pair_kim.html"><span class="doc">kim</span></a></td>
<tr class="row-odd"><td><a class="reference internal" href="pair_kim.html"><span class="doc">kim</span></a></td>
<td>PARAM_FREE_*&amp;#58i,j,...</td>
<td>global</td>
</tr>
@ -315,7 +319,7 @@ 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>
<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
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
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
@ -341,10 +345,10 @@ details.</p>
<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
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>
<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>
</pre></div>
</div>
<pre class="literal-block">
variable prefactor equal ramp(10,30)
fix 1 all adapt 1 pair soft a * * v_prefactor
</pre>
<hr class="docutils" />
<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
@ -380,14 +384,12 @@ constant).</p>
<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
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>
<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="n">v_size</span>
</pre></div>
</div>
</div>
<pre class="literal-block">
variable size equal ramp(1.0,0.1)
fix 1 center adapt 10 atom diameter v_size
</pre>
<hr class="docutils" />
<div class="section" id="restart-fix-modify-output-run-start-stop-minimize-info">
<h2>Restart, fix_modify, output, run start/stop, minimize info</h2>
<p><strong>Restart, fix_modify, output, run start/stop, minimize info:</strong></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>. None of the <a class="reference internal" href="fix_modify.html"><span class="doc">fix_modify</span></a> options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various <a class="reference internal" href="Section_howto.html#howto-15"><span class="std std-ref">output commands</span></a>. No parameter of this fix can

6
doc/html/pair_dipole.html
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@ -183,6 +183,7 @@ pair_coeff 2 3 1.0 1.0 2.5 4.0
<pre class="literal-block">
pair_style lj/sf/dipole/sf 9.0
pair_coeff * * 1.0 1.0
pair_coeff 2 3 1.0 1.0 2.5 4.0 scale 0.5
pair_coeff 2 3 1.0 1.0 2.5 4.0
</pre>
<pre class="literal-block">
@ -242,7 +243,10 @@ C.3 of <a class="reference internal" href="pair_gayberne.html#allen"><span class
<p>If one cutoff is specified in the pair_style command, it is used for
both the LJ and Coulombic (q,p) terms. If two cutoffs are specified,
they are used as cutoffs for the LJ and Coulombic (q,p) terms
respectively.</p>
respectively. This pair style also supports an optional <em>scale</em> keyword
as part of a pair_coeff statement, where the interactions can be
scaled according to this factor. This scale factor is also made available
for use with fix adapt.</p>
<p>Style <em>lj/cut/dipole/long</em> computes long-range point-dipole
interactions as discussed in <a class="reference internal" href="#toukmaji"><span class="std std-ref">(Toukmaji)</span></a>. Dipole-dipole,
dipole-charge, and charge-charge interactions are all supported, along

1
doc/src/fix_adapt.txt
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@ -110,6 +110,7 @@ meaning of these parameters:
"coul/long"_pair_coul.html: scale: type pairs:
"lj/cut"_pair_lj.html: epsilon,sigma: type pairs:
"lj/expand"_pair_lj_expand.html: epsilon,sigma,delta: type pairs:
"lj/sf/dipole/sf"_pair_dipole.html: epsilon,sigma,scale: type pairs:
"lubricate"_pair_lubricate.html: mu: global:
"gauss"_pair_gauss.html: a: type pairs:
"morse"_pair_morse.html: d0,r0,alpha: type pairs:

6
doc/src/pair_dipole.txt
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@ -41,6 +41,7 @@ pair_coeff 2 3 1.0 1.0 2.5 4.0 :pre
pair_style lj/sf/dipole/sf 9.0
pair_coeff * * 1.0 1.0
pair_coeff 2 3 1.0 1.0 2.5 4.0 scale 0.5
pair_coeff 2 3 1.0 1.0 2.5 4.0 :pre
pair_style lj/cut/dipole/long 10.0
@ -103,7 +104,10 @@ C.3 of "(Allen)"_#Allen.
If one cutoff is specified in the pair_style command, it is used for
both the LJ and Coulombic (q,p) terms. If two cutoffs are specified,
they are used as cutoffs for the LJ and Coulombic (q,p) terms
respectively.
respectively. This pair style also supports an optional {scale} keyword
as part of a pair_coeff statement, where the interactions can be
scaled according to this factor. This scale factor is also made available
for use with fix adapt.
Style {lj/cut/dipole/long} computes long-range point-dipole
interactions as discussed in "(Toukmaji)"_#Toukmaji. Dipole-dipole,