Commit a69e059b authored by sjplimp's avatar sjplimp Committed by GitHub
Browse files

Merge pull request #27 from akohlmey/small-bugfixes 

Collected small changes and bugfixes
parents dbc548dd 80c5b01b

doc/html/boundary.html

+9 −1
Original line number Diff line number Diff line
@@ -173,7 +173,15 @@ you have set the <a class="reference internal" href="thermo_modify.html"><span c 
allow for lost atoms.</p>

<p>For style <em>s</em>, the position of the face is set so as to encompass the

atoms in that dimension (shrink-wrapping), no matter how far they

move.</p>

move. Note that when the difference between the current box dimensions

and the shrink-wrap box dimensions is large, this can lead to lost

atoms at the beginning of a run when running in parallel. This is due

to the large change in the (global) box dimensions also causing

significant changes in the individual sub-domain sizes. If these

changes are farther than the communication cutoff, atoms will be lost.

This is best addressed by setting initial box dimensions to match the

shrink-wrapped dimensions more closely, by using <em>m</em> style boundaries

(see below).</p>

<p>For style <em>m</em>, shrink-wrapping occurs, but is bounded by the value

specified in the data or restart file or set by the

<a class="reference internal" href="create_box.html"><span class="doc">create_box</span></a> command.  For example, if the upper z

doc/html/compute_rdf.html

+12 −12
Original line number Diff line number Diff line
@@ -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

doc/html/fix_adapt.html

+27 −25
Original line number Diff line number Diff line
@@ -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

doc/html/pair_dipole.html

+31 −27
Original line number Diff line number Diff line
@@ -149,12 +149,12 @@ 
<h1>pair_style lj/long/dipole/long command</h1>

<div class="section" id="syntax">

<h2>Syntax</h2>

<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">dipole</span><span class="o">/</span><span class="n">cut</span> <span class="n">cutoff</span> <span class="p">(</span><span class="n">cutoff2</span><span class="p">)</span>

<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">sf</span><span class="o">/</span><span class="n">dipole</span><span class="o">/</span><span class="n">sf</span> <span class="n">cutoff</span> <span class="p">(</span><span class="n">cutoff2</span><span class="p">)</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">dipole</span><span class="o">/</span><span class="n">long</span> <span class="n">cutoff</span> <span class="p">(</span><span class="n">cutoff2</span><span class="p">)</span>

<span class="n">pair_style</span> <span class="n">lj</span><span class="o">/</span><span class="n">long</span><span class="o">/</span><span class="n">dipole</span><span class="o">/</span><span class="n">long</span> <span class="n">flag_lj</span> <span class="n">flag_coul</span> <span class="n">cutoff</span> <span class="p">(</span><span class="n">cutoff2</span><span class="p">)</span>

</pre></div>

</div>

<pre class="literal-block">

pair_style lj/cut/dipole/cut cutoff (cutoff2)

pair_style lj/sf/dipole/sf cutoff (cutoff2)

pair_style lj/cut/dipole/long cutoff (cutoff2)

pair_style lj/long/dipole/long flag_lj flag_coul cutoff (cutoff2)

</pre>

<ul class="simple">

<li>cutoff = global cutoff LJ (and Coulombic if only 1 arg) (distance units)</li>

<li>cutoff2 = global cutoff for Coulombic and dipole (optional) (distance units)</li>
@@ -175,26 +175,27 @@ 
</div>

<div class="section" id="examples">

<h2>Examples</h2>

<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">dipole</span><span class="o">/</span><span class="n">cut</span> <span class="mf">10.0</span>

<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">1.0</span>

<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span> <span class="mf">4.0</span>

</pre></div>

</div>

<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">sf</span><span class="o">/</span><span class="n">dipole</span><span class="o">/</span><span class="n">sf</span> <span class="mf">9.0</span>

<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">1.0</span>

<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span> <span class="mf">4.0</span>

</pre></div>

</div>

<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">dipole</span><span class="o">/</span><span class="n">long</span> <span class="mf">10.0</span>

<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">1.0</span>

<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span> <span class="mf">4.0</span>

</pre></div>

</div>

<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">long</span><span class="o">/</span><span class="n">dipole</span><span class="o">/</span><span class="n">long</span> <span class="n">long</span> <span class="n">long</span> <span class="mf">3.5</span> <span class="mf">10.0</span>

<span class="n">pair_coeff</span> <span class="o">*</span> <span class="o">*</span> <span class="mf">1.0</span> <span class="mf">1.0</span>

<span class="n">pair_coeff</span> <span class="mi">2</span> <span class="mi">3</span> <span class="mf">1.0</span> <span class="mf">1.0</span> <span class="mf">2.5</span> <span class="mf">4.0</span>

</pre></div>

</div>

<pre class="literal-block">

pair_style lj/cut/dipole/cut 10.0

pair_coeff * * 1.0 1.0

pair_coeff 2 3 1.0 1.0 2.5 4.0

</pre>

<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">

pair_style lj/cut/dipole/long 10.0

pair_coeff * * 1.0 1.0

pair_coeff 2 3 1.0 1.0 2.5 4.0

</pre>

<pre class="literal-block">

pair_style lj/long/dipole/long long long 3.5 10.0

pair_coeff * * 1.0 1.0

pair_coeff 2 3 1.0 1.0 2.5 4.0

</pre>

</div>

<div class="section" id="description">

<h2>Description</h2>
@@ -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

doc/src/boundary.txt

+9 −1
Original line number Diff line number Diff line
@@ -54,7 +54,15 @@ allow for lost atoms. 


For style {s}, the position of the face is set so as to encompass the

atoms in that dimension (shrink-wrapping), no matter how far they

move.

move. Note that when the difference between the current box dimensions

and the shrink-wrap box dimensions is large, this can lead to lost

atoms at the beginning of a run when running in parallel. This is due

to the large change in the (global) box dimensions also causing

significant changes in the individual sub-domain sizes. If these

changes are farther than the communication cutoff, atoms will be lost.

This is best addressed by setting initial box dimensions to match the

shrink-wrapped dimensions more closely, by using {m} style boundaries

(see below).



For style {m}, shrink-wrapping occurs, but is bounded by the value

specified in the data or restart file or set by the

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