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<li class="toctree-l3"><a class="reference internal" href="Developer_write_pair.html">4.8.1. Writing new pair styles</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Developer_write_pair.html#case-1-a-pairwise-additive-model">4.8.3. Case 1: a pairwise additive model</a></li>
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<li class="toctree-l3"><a class="reference internal" href="Developer_write_command.html#case-1-implementing-the-geturl-command">4.8.9. Case 1: Implementing the geturl command</a></li>
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<li class="toctree-l2"><a class="reference internal" href="Developer_utils.html#communication-buffer-coding-with-ubuf">4.22. Communication buffer coding with <em>ubuf</em></a></li>
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<li class="toctree-l2"><a class="reference internal" href="Developer_grid.html">4.23. Use of distributed grids within style classes</a></li>
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<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fix Styles</a></li>
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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
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<section id="writing-a-new-fix-style">
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<h1><span class="section-number">4.8.7. </span>Writing a new fix style<a class="headerlink" href="#writing-a-new-fix-style" title="Link to this heading"></a></h1>
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<p>Writing fix styles is a flexible way of extending LAMMPS. Users can
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implement many things using fixes. Some fix styles are only used
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internally to support compute styles or pair styles:</p>
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<ul class="simple">
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<li><p>change particles attributes (positions, velocities, forces, etc.). Examples: <code class="docutils literal notranslate"><span class="pre">FixNVE</span></code>, <code class="docutils literal notranslate"><span class="pre">FixFreeze</span></code>.</p></li>
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<li><p>read or write data. Example: <code class="docutils literal notranslate"><span class="pre">FixRestart</span></code>.</p></li>
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<li><p>adding or modifying properties due to geometry. Example: <code class="docutils literal notranslate"><span class="pre">FixWall</span></code>.</p></li>
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<li><p>interacting with other subsystems or external code: Examples: <code class="docutils literal notranslate"><span class="pre">FixTTM</span></code>, <code class="docutils literal notranslate"><span class="pre">FixExternal</span></code>, <code class="docutils literal notranslate"><span class="pre">FixMDI</span></code></p></li>
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<li><p>saving information for analysis or future use (previous positions,
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for instance). Examples: <code class="docutils literal notranslate"><span class="pre">FixAveTime</span></code>, <code class="docutils literal notranslate"><span class="pre">FixStoreState</span></code>.</p></li>
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</ul>
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<p>All fixes are derived from the <code class="docutils literal notranslate"><span class="pre">Fix</span></code> base class and must have a
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constructor with the signature: <code class="docutils literal notranslate"><span class="pre">FixPrintVel(class</span> <span class="pre">LAMMPS</span> <span class="pre">*,</span> <span class="pre">int,</span> <span class="pre">char</span> <span class="pre">**)</span></code>.</p>
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<p>Every fix must be registered in LAMMPS by writing the following lines
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of code in the header before include guards:</p>
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<div class="highlight-c++ notranslate"><div class="highlight"><pre><span></span><span class="cp">#ifdef FIX_CLASS</span>
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<span class="c1">// clang-format off</span>
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<span class="n">FixStyle</span><span class="p">(</span><span class="n">print</span><span class="o">/</span><span class="n">vel</span><span class="p">,</span><span class="n">FixPrintVel</span><span class="p">);</span>
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<span class="c1">// clang-format on</span>
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<span class="cp">#else</span>
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<span class="cm">/* the definition of the FixPrintVel class comes here */</span>
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<span class="p">...</span>
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<span class="cp">#endif</span>
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</pre></div>
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</div>
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<p>Where <code class="docutils literal notranslate"><span class="pre">print/vel</span></code> is the style name of your fix in the input script and
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<code class="docutils literal notranslate"><span class="pre">FixPrintVel</span></code> is the name of the class. The header file would be called
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<code class="docutils literal notranslate"><span class="pre">fix_print_vel.h</span></code> and the implementation file <code class="docutils literal notranslate"><span class="pre">fix_print_vel.cpp</span></code>.
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These conventions allow LAMMPS to automatically integrate it into the
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executable when compiling and associate your new fix class with the designated
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keyword when it parses the input script.</p>
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<p>Let’s write a simple fix which will print the average velocity at the end
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of each timestep. First of all, implement a constructor:</p>
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<div class="highlight-c++ notranslate"><div class="highlight"><pre><span></span><span class="n">FixPrintVel</span><span class="o">::</span><span class="n">FixPrintVel</span><span class="p">(</span><span class="n">LAMMPS</span><span class="w"> </span><span class="o">*</span><span class="n">lmp</span><span class="p">,</span><span class="w"> </span><span class="kt">int</span><span class="w"> </span><span class="n">narg</span><span class="p">,</span><span class="w"> </span><span class="kt">char</span><span class="w"> </span><span class="o">**</span><span class="n">arg</span><span class="p">)</span>
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<span class="o">:</span><span class="w"> </span><span class="n">Fix</span><span class="p">(</span><span class="n">lmp</span><span class="p">,</span><span class="w"> </span><span class="n">narg</span><span class="p">,</span><span class="w"> </span><span class="n">arg</span><span class="p">)</span>
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<span class="p">{</span>
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<span class="w"> </span><span class="k">if</span><span class="w"> </span><span class="p">(</span><span class="n">narg</span><span class="w"> </span><span class="o"><</span><span class="w"> </span><span class="mi">4</span><span class="p">)</span><span class="w"> </span><span class="n">utils</span><span class="o">::</span><span class="n">missing_cmd_args</span><span class="p">(</span><span class="n">FLERR</span><span class="p">,</span><span class="w"> </span><span class="s">"fix print/vel"</span><span class="p">,</span><span class="w"> </span><span class="n">error</span><span class="p">);</span>
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<span class="w"> </span><span class="n">nevery</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">utils</span><span class="o">::</span><span class="n">inumeric</span><span class="p">(</span><span class="n">FLERR</span><span class="p">,</span><span class="n">arg</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span><span class="nb">false</span><span class="p">,</span><span class="n">lmp</span><span class="p">);</span>
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<span class="w"> </span><span class="k">if</span><span class="w"> </span><span class="p">(</span><span class="n">nevery</span><span class="w"> </span><span class="o"><=</span><span class="w"> </span><span class="mi">0</span><span class="p">)</span>
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<span class="w"> </span><span class="n">error</span><span class="o">-></span><span class="n">all</span><span class="p">(</span><span class="n">FLERR</span><span class="p">,</span><span class="s">"Illegal fix print/vel nevery value: {}"</span><span class="p">,</span><span class="w"> </span><span class="n">nevery</span><span class="p">);</span>
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<span class="p">}</span>
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</pre></div>
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</div>
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<p>In the constructor you should parse the fix arguments which are
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specified in the script. All fixes have pretty much the same syntax:
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<code class="docutils literal notranslate"><span class="pre">fix</span> <span class="pre"><fix-ID></span> <span class="pre"><fix</span> <span class="pre">group></span> <span class="pre"><fix</span> <span class="pre">name></span> <span class="pre"><fix</span> <span class="pre">arguments</span> <span class="pre">...></span></code>. The first 3
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parameters are parsed by Fix base class constructor, while <code class="docutils literal notranslate"><span class="pre"><fix</span>
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<span class="pre">arguments></span></code> should be parsed by you. In our case, we need to specify
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how often we want to print an average velocity. For instance, once in 50
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timesteps: <code class="docutils literal notranslate"><span class="pre">fix</span> <span class="pre">1</span> <span class="pre">print/vel</span> <span class="pre">50</span></code>. There is a special variable in the
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Fix class called <code class="docutils literal notranslate"><span class="pre">nevery</span></code> which specifies how often the method
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<code class="docutils literal notranslate"><span class="pre">end_of_step()</span></code> is called. Thus all we need to do is just set it up.</p>
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<p>The next method we need to implement is <code class="docutils literal notranslate"><span class="pre">setmask()</span></code>:</p>
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<div class="highlight-c++ notranslate"><div class="highlight"><pre><span></span><span class="kt">int</span><span class="w"> </span><span class="nf">FixPrintVel::setmask</span><span class="p">()</span>
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<span class="p">{</span>
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<span class="w"> </span><span class="kt">int</span><span class="w"> </span><span class="n">mask</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="mi">0</span><span class="p">;</span>
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<span class="w"> </span><span class="n">mask</span><span class="w"> </span><span class="o">|=</span><span class="w"> </span><span class="n">FixConst</span><span class="o">::</span><span class="n">END_OF_STEP</span><span class="p">;</span>
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<span class="w"> </span><span class="k">return</span><span class="w"> </span><span class="n">mask</span><span class="p">;</span>
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<span class="p">}</span>
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</pre></div>
|
||
</div>
|
||
<p>Here the we specify which methods of the fix should be called during
|
||
<a class="reference internal" href="Developer_flow.html"><span class="doc">execution of a timestep</span></a>. The constant
|
||
<code class="docutils literal notranslate"><span class="pre">END_OF_STEP</span></code> corresponds to the <code class="docutils literal notranslate"><span class="pre">end_of_step()</span></code> method.</p>
|
||
<div class="highlight-c++ notranslate"><div class="highlight"><pre><span></span><span class="kt">void</span><span class="w"> </span><span class="nf">FixPrintVel::end_of_step</span><span class="p">()</span>
|
||
<span class="p">{</span>
|
||
<span class="w"> </span><span class="c1">// for add3, scale3</span>
|
||
<span class="w"> </span><span class="k">using</span><span class="w"> </span><span class="k">namespace</span><span class="w"> </span><span class="nn">MathExtra</span><span class="p">;</span>
|
||
|
||
<span class="w"> </span><span class="kt">double</span><span class="o">**</span><span class="w"> </span><span class="n">v</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">atom</span><span class="o">-></span><span class="n">v</span><span class="p">;</span>
|
||
<span class="w"> </span><span class="kt">int</span><span class="w"> </span><span class="n">nlocal</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">atom</span><span class="o">-></span><span class="n">nlocal</span><span class="p">;</span>
|
||
<span class="w"> </span><span class="kt">double</span><span class="w"> </span><span class="n">localAvgVel</span><span class="p">[</span><span class="mi">4</span><span class="p">];</span><span class="w"> </span><span class="c1">// 4th element for particles count</span>
|
||
<span class="w"> </span><span class="n">memset</span><span class="p">(</span><span class="n">localAvgVel</span><span class="p">,</span><span class="w"> </span><span class="mi">0</span><span class="p">,</span><span class="w"> </span><span class="mi">4</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="k">sizeof</span><span class="p">(</span><span class="kt">double</span><span class="p">));</span>
|
||
<span class="w"> </span><span class="k">for</span><span class="w"> </span><span class="p">(</span><span class="kt">int</span><span class="w"> </span><span class="n">particleInd</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="mi">0</span><span class="p">;</span><span class="w"> </span><span class="n">particleInd</span><span class="w"> </span><span class="o"><</span><span class="w"> </span><span class="n">nlocal</span><span class="p">;</span><span class="w"> </span><span class="o">++</span><span class="n">particleInd</span><span class="p">)</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="n">add3</span><span class="p">(</span><span class="n">localAvgVel</span><span class="p">,</span><span class="w"> </span><span class="n">v</span><span class="p">[</span><span class="n">particleInd</span><span class="p">],</span><span class="w"> </span><span class="n">localAvgVel</span><span class="p">);</span>
|
||
<span class="w"> </span><span class="p">}</span>
|
||
<span class="w"> </span><span class="n">localAvgVel</span><span class="p">[</span><span class="mi">3</span><span class="p">]</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">nlocal</span><span class="p">;</span>
|
||
<span class="w"> </span><span class="kt">double</span><span class="w"> </span><span class="n">globalAvgVel</span><span class="p">[</span><span class="mi">4</span><span class="p">];</span>
|
||
<span class="w"> </span><span class="n">memset</span><span class="p">(</span><span class="n">globalAvgVel</span><span class="p">,</span><span class="w"> </span><span class="mi">0</span><span class="p">,</span><span class="w"> </span><span class="mi">4</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="k">sizeof</span><span class="p">(</span><span class="kt">double</span><span class="p">));</span>
|
||
<span class="w"> </span><span class="n">MPI_Allreduce</span><span class="p">(</span><span class="n">localAvgVel</span><span class="p">,</span><span class="w"> </span><span class="n">globalAvgVel</span><span class="p">,</span><span class="w"> </span><span class="mi">4</span><span class="p">,</span><span class="w"> </span><span class="n">MPI_DOUBLE</span><span class="p">,</span><span class="w"> </span><span class="n">MPI_SUM</span><span class="p">,</span><span class="w"> </span><span class="n">world</span><span class="p">);</span>
|
||
<span class="w"> </span><span class="n">scale3</span><span class="p">(</span><span class="mf">1.0</span><span class="w"> </span><span class="o">/</span><span class="w"> </span><span class="n">globalAvgVel</span><span class="p">[</span><span class="mi">3</span><span class="p">],</span><span class="w"> </span><span class="n">globalAvgVel</span><span class="p">);</span>
|
||
<span class="w"> </span><span class="k">if</span><span class="w"> </span><span class="p">((</span><span class="n">comm</span><span class="o">-></span><span class="n">me</span><span class="w"> </span><span class="o">==</span><span class="w"> </span><span class="mi">0</span><span class="p">)</span><span class="w"> </span><span class="o">&&</span><span class="w"> </span><span class="n">screen</span><span class="p">)</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="n">fmt</span><span class="o">::</span><span class="n">print</span><span class="p">(</span><span class="n">screen</span><span class="p">,</span><span class="s">"{}, {}, {}</span><span class="se">\n</span><span class="s">"</span><span class="p">,</span>
|
||
<span class="w"> </span><span class="n">globalAvgVel</span><span class="p">[</span><span class="mi">0</span><span class="p">],</span><span class="w"> </span><span class="n">globalAvgVel</span><span class="p">[</span><span class="mi">1</span><span class="p">],</span><span class="w"> </span><span class="n">globalAvgVel</span><span class="p">[</span><span class="mi">2</span><span class="p">]);</span>
|
||
<span class="w"> </span><span class="p">}</span>
|
||
<span class="p">}</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>In the code above, we use MathExtra routines defined in
|
||
<code class="docutils literal notranslate"><span class="pre">math_extra.h</span></code>. There are bunch of math functions to work with
|
||
arrays of doubles as with math vectors. It is also important to note
|
||
that LAMMPS code should always assume to be run in parallel and that
|
||
atom data is thus distributed across the MPI ranks. Thus you can
|
||
only process data from local atoms directly and need to use MPI library
|
||
calls to combine or exchange data. For serial execution, LAMMPS
|
||
comes bundled with the MPI STUBS library that contains the MPI library
|
||
function calls in dummy versions that only work for a single MPI rank.</p>
|
||
<p>In this code we use an instance of Atom class. This object is stored
|
||
in the Pointers class (see <code class="docutils literal notranslate"><span class="pre">pointers.h</span></code>) which is the base class of
|
||
the Fix base class. This object contains references to various class
|
||
instances (the original instances are created and held by the LAMMPS
|
||
class) with all global information about the simulation system.
|
||
Data from the Pointers class is available to all classes inherited from
|
||
it using protected inheritance. Hence when you write you own class,
|
||
which is going to use LAMMPS data, don’t forget to inherit from Pointers
|
||
or pass a Pointer to it to all functions that need access. When writing
|
||
fixes we inherit from class Fix which is inherited from Pointers so
|
||
there is no need to inherit from it directly.</p>
|
||
<p>The code above computes average velocity for all particles in the
|
||
simulation. Yet you have one unused parameter in fix call from the
|
||
script: <code class="docutils literal notranslate"><span class="pre">group_name</span></code>. This parameter specifies the group of atoms
|
||
used in the fix. So we should compute the average for all particles in the
|
||
simulation only if <code class="docutils literal notranslate"><span class="pre">group_name</span> <span class="pre">==</span> <span class="pre">"all"</span></code>, but it can be any group.
|
||
The group membership information of an atom is contained in the <em>mask</em>
|
||
property of an atom and the bit corresponding to a given group is
|
||
stored in the groupbit variable which is defined in Fix base class:</p>
|
||
<div class="highlight-c++ notranslate"><div class="highlight"><pre><span></span><span class="k">for</span><span class="w"> </span><span class="p">(</span><span class="kt">int</span><span class="w"> </span><span class="n">i</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="mi">0</span><span class="p">;</span><span class="w"> </span><span class="n">i</span><span class="w"> </span><span class="o"><</span><span class="w"> </span><span class="n">nlocal</span><span class="p">;</span><span class="w"> </span><span class="o">++</span><span class="n">i</span><span class="p">)</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="k">if</span><span class="w"> </span><span class="p">(</span><span class="n">atom</span><span class="o">-></span><span class="n">mask</span><span class="p">[</span><span class="n">i</span><span class="p">]</span><span class="w"> </span><span class="o">&</span><span class="w"> </span><span class="n">groupbit</span><span class="p">)</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="c1">// Do all job here</span>
|
||
<span class="w"> </span><span class="p">}</span>
|
||
<span class="p">}</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>Class Atom encapsulates atoms positions, velocities, forces, etc. Users
|
||
can access them using the particle index. Note, that particle indexes are
|
||
usually changed every few timesteps because of neighbor list rebuilds
|
||
and spatial sorting (to improve cache efficiency).</p>
|
||
<p>Let us consider another Fix example: We want to have a fix which stores
|
||
atoms position from the previous time step in your fix. The local atoms
|
||
indexes may not be valid on the next iteration. In order to handle
|
||
this situation there are several methods which should be implemented:</p>
|
||
<ul class="simple">
|
||
<li><p><code class="docutils literal notranslate"><span class="pre">double</span> <span class="pre">memory_usage()</span></code>: return how much memory the fix uses (optional)</p></li>
|
||
<li><p><code class="docutils literal notranslate"><span class="pre">void</span> <span class="pre">grow_arrays(int)</span></code>: do reallocation of the per-particle arrays in your fix</p></li>
|
||
<li><p><code class="docutils literal notranslate"><span class="pre">void</span> <span class="pre">copy_arrays(int</span> <span class="pre">i,</span> <span class="pre">int</span> <span class="pre">j,</span> <span class="pre">int</span> <span class="pre">delflag)</span></code>: copy i-th per-particle
|
||
information to j-th particle position. Used when atom sorting is performed.
|
||
if delflag is set and atom j owns a body, move the body information to atom i.</p></li>
|
||
<li><p><code class="docutils literal notranslate"><span class="pre">void</span> <span class="pre">set_arrays(int</span> <span class="pre">i)</span></code>: sets i-th particle related information to zero</p></li>
|
||
</ul>
|
||
<p>Note, that if your class implements these methods, it must add calls of
|
||
add_callback and delete_callback to the constructor and destructor. Since we want
|
||
to store positions of atoms from the previous timestep, we need to add
|
||
<code class="docutils literal notranslate"><span class="pre">double**</span> <span class="pre">xold</span></code> to the header file. Than add allocation code
|
||
to the constructor:</p>
|
||
<div class="highlight-c++ notranslate"><div class="highlight"><pre><span></span><span class="n">FixSavePos</span><span class="o">::</span><span class="n">FixSavePos</span><span class="p">(</span><span class="n">LAMMPS</span><span class="w"> </span><span class="o">*</span><span class="n">lmp</span><span class="p">,</span><span class="w"> </span><span class="kt">int</span><span class="w"> </span><span class="n">narg</span><span class="p">,</span><span class="w"> </span><span class="kt">char</span><span class="w"> </span><span class="o">**</span><span class="n">arg</span><span class="p">),</span><span class="w"> </span><span class="n">xold</span><span class="p">(</span><span class="k">nullptr</span><span class="p">)</span>
|
||
<span class="p">{</span>
|
||
<span class="c1">//...</span>
|
||
<span class="w"> </span><span class="n">memory</span><span class="o">-></span><span class="n">create</span><span class="p">(</span><span class="n">xold</span><span class="p">,</span><span class="w"> </span><span class="n">atom</span><span class="o">-></span><span class="n">nmax</span><span class="p">,</span><span class="w"> </span><span class="mi">3</span><span class="p">,</span><span class="w"> </span><span class="s">"FixSavePos:x"</span><span class="p">);</span>
|
||
<span class="w"> </span><span class="n">atom</span><span class="o">-></span><span class="n">add_callback</span><span class="p">(</span><span class="mi">0</span><span class="p">);</span>
|
||
<span class="p">}</span>
|
||
|
||
<span class="n">FixSavePos</span><span class="o">::~</span><span class="n">FixSavePos</span><span class="p">()</span><span class="w"> </span><span class="p">{</span>
|
||
<span class="w"> </span><span class="n">atom</span><span class="o">-></span><span class="n">delete_callback</span><span class="p">(</span><span class="n">id</span><span class="p">,</span><span class="w"> </span><span class="mi">0</span><span class="p">);</span>
|
||
<span class="w"> </span><span class="n">memory</span><span class="o">-></span><span class="n">destroy</span><span class="p">(</span><span class="n">xold</span><span class="p">);</span>
|
||
<span class="p">}</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>Implement the aforementioned methods:</p>
|
||
<div class="highlight-c++ notranslate"><div class="highlight"><pre><span></span><span class="kt">double</span><span class="w"> </span><span class="nf">FixSavePos::memory_usage</span><span class="p">()</span>
|
||
<span class="p">{</span>
|
||
<span class="w"> </span><span class="kt">int</span><span class="w"> </span><span class="n">nmax</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">atom</span><span class="o">-></span><span class="n">nmax</span><span class="p">;</span>
|
||
<span class="w"> </span><span class="kt">double</span><span class="w"> </span><span class="n">bytes</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="mf">0.0</span><span class="p">;</span>
|
||
<span class="w"> </span><span class="n">bytes</span><span class="w"> </span><span class="o">+=</span><span class="w"> </span><span class="n">nmax</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="mi">3</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="k">sizeof</span><span class="p">(</span><span class="kt">double</span><span class="p">);</span>
|
||
<span class="w"> </span><span class="k">return</span><span class="w"> </span><span class="n">bytes</span><span class="p">;</span>
|
||
<span class="p">}</span>
|
||
|
||
<span class="kt">void</span><span class="w"> </span><span class="nf">FixSavePos::grow_arrays</span><span class="p">(</span><span class="kt">int</span><span class="w"> </span><span class="n">nmax</span><span class="p">)</span>
|
||
<span class="p">{</span>
|
||
<span class="w"> </span><span class="n">memory</span><span class="o">-></span><span class="n">grow</span><span class="p">(</span><span class="n">xold</span><span class="p">,</span><span class="w"> </span><span class="n">nmax</span><span class="p">,</span><span class="w"> </span><span class="mi">3</span><span class="p">,</span><span class="w"> </span><span class="s">"FixSavePos:xold"</span><span class="p">);</span>
|
||
<span class="p">}</span>
|
||
|
||
<span class="kt">void</span><span class="w"> </span><span class="nf">FixSavePos::copy_arrays</span><span class="p">(</span><span class="kt">int</span><span class="w"> </span><span class="n">i</span><span class="p">,</span><span class="w"> </span><span class="kt">int</span><span class="w"> </span><span class="n">j</span><span class="p">,</span><span class="w"> </span><span class="kt">int</span><span class="w"> </span><span class="n">delflag</span><span class="p">)</span>
|
||
<span class="p">{</span>
|
||
<span class="w"> </span><span class="n">memcpy</span><span class="p">(</span><span class="n">xold</span><span class="p">[</span><span class="n">j</span><span class="p">],</span><span class="w"> </span><span class="n">xold</span><span class="p">[</span><span class="n">i</span><span class="p">],</span><span class="w"> </span><span class="k">sizeof</span><span class="p">(</span><span class="kt">double</span><span class="p">)</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="mi">3</span><span class="p">);</span>
|
||
<span class="p">}</span>
|
||
|
||
<span class="kt">void</span><span class="w"> </span><span class="nf">FixSavePos::set_arrays</span><span class="p">(</span><span class="kt">int</span><span class="w"> </span><span class="n">i</span><span class="p">)</span>
|
||
<span class="p">{</span>
|
||
<span class="w"> </span><span class="n">memset</span><span class="p">(</span><span class="n">xold</span><span class="p">[</span><span class="n">i</span><span class="p">],</span><span class="w"> </span><span class="mi">0</span><span class="p">,</span><span class="w"> </span><span class="k">sizeof</span><span class="p">(</span><span class="kt">double</span><span class="p">)</span><span class="w"> </span><span class="o">*</span><span class="w"> </span><span class="mi">3</span><span class="p">);</span>
|
||
<span class="p">}</span>
|
||
|
||
<span class="kt">int</span><span class="w"> </span><span class="nf">FixSavePos::pack_exchange</span><span class="p">(</span><span class="kt">int</span><span class="w"> </span><span class="n">i</span><span class="p">,</span><span class="w"> </span><span class="kt">double</span><span class="w"> </span><span class="o">*</span><span class="n">buf</span><span class="p">)</span>
|
||
<span class="p">{</span>
|
||
<span class="w"> </span><span class="kt">int</span><span class="w"> </span><span class="n">m</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="mi">0</span><span class="p">;</span>
|
||
<span class="w"> </span><span class="n">buf</span><span class="p">[</span><span class="n">m</span><span class="o">++</span><span class="p">]</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">xold</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="mi">0</span><span class="p">];</span>
|
||
<span class="w"> </span><span class="n">buf</span><span class="p">[</span><span class="n">m</span><span class="o">++</span><span class="p">]</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">xold</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="mi">1</span><span class="p">];</span>
|
||
<span class="w"> </span><span class="n">buf</span><span class="p">[</span><span class="n">m</span><span class="o">++</span><span class="p">]</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">xold</span><span class="p">[</span><span class="n">i</span><span class="p">][</span><span class="mi">2</span><span class="p">];</span>
|
||
|
||
<span class="w"> </span><span class="k">return</span><span class="w"> </span><span class="n">m</span><span class="p">;</span>
|
||
<span class="p">}</span>
|
||
|
||
<span class="kt">int</span><span class="w"> </span><span class="nf">FixSavePos::unpack_exchange</span><span class="p">(</span><span class="kt">int</span><span class="w"> </span><span class="n">nlocal</span><span class="p">,</span><span class="w"> </span><span class="kt">double</span><span class="w"> </span><span class="o">*</span><span class="n">buf</span><span class="p">)</span>
|
||
<span class="p">{</span>
|
||
<span class="w"> </span><span class="kt">int</span><span class="w"> </span><span class="n">m</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="mi">0</span><span class="p">;</span>
|
||
<span class="w"> </span><span class="n">xold</span><span class="p">[</span><span class="n">nlocal</span><span class="p">][</span><span class="mi">0</span><span class="p">]</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">buf</span><span class="p">[</span><span class="n">m</span><span class="o">++</span><span class="p">];</span>
|
||
<span class="w"> </span><span class="n">xold</span><span class="p">[</span><span class="n">nlocal</span><span class="p">][</span><span class="mi">1</span><span class="p">]</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">buf</span><span class="p">[</span><span class="n">m</span><span class="o">++</span><span class="p">];</span>
|
||
<span class="w"> </span><span class="n">xold</span><span class="p">[</span><span class="n">nlocal</span><span class="p">][</span><span class="mi">2</span><span class="p">]</span><span class="w"> </span><span class="o">=</span><span class="w"> </span><span class="n">buf</span><span class="p">[</span><span class="n">m</span><span class="o">++</span><span class="p">];</span>
|
||
|
||
<span class="w"> </span><span class="k">return</span><span class="w"> </span><span class="n">m</span><span class="p">;</span>
|
||
<span class="p">}</span>
|
||
</pre></div>
|
||
</div>
|
||
<p>Now, a little bit about memory allocation. We use the Memory class which
|
||
is just a bunch of template functions for allocating 1D and 2D
|
||
arrays. So you need to add include <code class="docutils literal notranslate"><span class="pre">memory.h</span></code> to have access to them.</p>
|
||
<p>Finally, if you need to write/read some global information used in
|
||
your fix to the restart file, you might do it by setting the flag
|
||
<code class="docutils literal notranslate"><span class="pre">restart_global</span> <span class="pre">=</span> <span class="pre">1</span></code> in the constructor and implementing methods
|
||
<code class="docutils literal notranslate"><span class="pre">void</span> <span class="pre">write_restart(FILE</span> <span class="pre">*fp)</span></code> and <code class="docutils literal notranslate"><span class="pre">void</span> <span class="pre">restart(char</span> <span class="pre">*buf)</span></code>.
|
||
If, in addition, you want to write the per-atom property to restart
|
||
files then these additional settings and functions are needed:</p>
|
||
<ul class="simple">
|
||
<li><p>a fix flag indicating this needs to be set <code class="docutils literal notranslate"><span class="pre">restart_peratom</span> <span class="pre">=</span> <span class="pre">1;</span></code></p></li>
|
||
<li><p><code class="docutils literal notranslate"><span class="pre">atom->add_callback()</span></code> and <code class="docutils literal notranslate"><span class="pre">atom->delete_callback()</span></code> must be called
|
||
a second time with the final argument set to 1 instead of 0 (indicating
|
||
restart processing instead of per-atom data memory management).</p></li>
|
||
<li><p>the functions <code class="docutils literal notranslate"><span class="pre">void</span> <span class="pre">pack_restart(int</span> <span class="pre">i,</span> <span class="pre">double</span> <span class="pre">*buf)</span></code> and
|
||
<code class="docutils literal notranslate"><span class="pre">void</span> <span class="pre">unpack_restart(int</span> <span class="pre">nlocal,</span> <span class="pre">int</span> <span class="pre">nth)</span></code> need to be implemented</p></li>
|
||
</ul>
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