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  <div class="section" id="au7-in-cu-111-with-emt">
<span id="au-on-cu-search"></span><h1>Au7 in Cu(111) with EMT<a class="headerlink" href="#au7-in-cu-111-with-emt" title="Permalink to this headline"></a></h1>
<p>In this tutorial we carry out a search for Au7-clusters on
the Cu(111) surface.</p>
<p>In this search we will utilize an <code class="xref py py-class docutils literal notranslate"><span class="pre">OperationConstraint</span></code>
to constraint the <code class="xref py py-class docutils literal notranslate"><span class="pre">RattleMutation</span></code> to only rattle the
atoms within a certain box in space that we define.</p>
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<p>The following script <a class="reference download internal" download="" href="../../_downloads/3cb85bca7334a25d0c7c987644b7693e/Au7_on_Cu111.py"><code class="xref download docutils literal notranslate"><span class="pre">Au7_on_Cu111.py</span></code></a> is used to carry
out the constrainted search:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span> <span class="nn">numpy</span> <span class="k">as</span> <span class="nn">np</span>

<span class="kn">from</span> <span class="nn">ase.build</span> <span class="k">import</span> <span class="n">fcc111</span>
<span class="kn">from</span> <span class="nn">ase.constraints</span> <span class="k">import</span> <span class="n">FixAtoms</span>
<span class="kn">from</span> <span class="nn">ase.calculators.emt</span> <span class="k">import</span> <span class="n">EMT</span>

<span class="kn">from</span> <span class="nn">gofee.candidates</span> <span class="k">import</span> <span class="n">CandidateGenerator</span><span class="p">,</span> <span class="n">StartGenerator</span><span class="p">,</span> <span class="n">RattleMutation</span><span class="p">,</span> <span class="n">PermutationMutation</span>
<span class="kn">from</span> <span class="nn">gofee.utils</span> <span class="k">import</span> <span class="n">OperationConstraint</span>
<span class="kn">from</span> <span class="nn">gofee</span> <span class="k">import</span> <span class="n">GOFEE</span>

<span class="c1">### Define calculator ###</span>
<span class="n">calc</span> <span class="o">=</span> <span class="n">EMT</span><span class="p">()</span>

<span class="c1">### Set up system ###</span>
<span class="c1"># 1-layer fixed Cu(111) slab</span>
<span class="n">template</span> <span class="o">=</span> <span class="n">fcc111</span><span class="p">(</span><span class="s1">&#39;Cu&#39;</span><span class="p">,</span> <span class="n">size</span><span class="o">=</span><span class="p">(</span><span class="mi">5</span><span class="p">,</span> <span class="mi">5</span><span class="p">,</span> <span class="mi">1</span><span class="p">),</span> <span class="n">vacuum</span><span class="o">=</span><span class="mf">10.0</span><span class="p">)</span>
<span class="n">c</span> <span class="o">=</span> <span class="n">FixAtoms</span><span class="p">(</span><span class="n">indices</span><span class="o">=</span><span class="n">np</span><span class="o">.</span><span class="n">arange</span><span class="p">(</span><span class="nb">len</span><span class="p">(</span><span class="n">template</span><span class="p">)))</span>
<span class="n">template</span><span class="o">.</span><span class="n">set_constraint</span><span class="p">(</span><span class="n">c</span><span class="p">)</span>

<span class="c1"># Stoichiometry of atoms to be placed</span>
<span class="n">stoichiometry</span> <span class="o">=</span> <span class="mi">7</span><span class="o">*</span><span class="p">[</span><span class="mi">79</span><span class="p">]</span>

<span class="c1">## Box for startgenerator and rattle-mutation</span>
<span class="n">k</span> <span class="o">=</span> <span class="mf">0.2</span>  <span class="c1"># Shrinkage fraction from each side of the box in v[0] and v[1] directions.</span>
<span class="n">cell</span> <span class="o">=</span> <span class="n">template</span><span class="o">.</span><span class="n">get_cell</span><span class="p">()</span>
<span class="c1"># Initialize box with cell</span>
<span class="n">v</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="n">cell</span><span class="p">)</span>
<span class="c1"># Set height of box</span>
<span class="n">v</span><span class="p">[</span><span class="mi">2</span><span class="p">][</span><span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="mi">5</span>
<span class="c1"># Shrink box in v[0] and v[1] directions</span>
<span class="n">v</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">*=</span> <span class="p">(</span><span class="mi">1</span><span class="o">-</span><span class="mi">2</span><span class="o">*</span><span class="n">k</span><span class="p">)</span>
<span class="n">v</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">*=</span> <span class="p">(</span><span class="mi">1</span><span class="o">-</span><span class="mi">2</span><span class="o">*</span><span class="n">k</span><span class="p">)</span>
<span class="c1"># Chose anker point p0 so box in centered in v[0] and v[1] directions.</span>
<span class="n">z_max_slab</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">template</span><span class="o">.</span><span class="n">get_positions</span><span class="p">()[:,</span><span class="mi">2</span><span class="p">])</span>
<span class="n">p0</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">((</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="n">z_max_slab</span><span class="o">+</span><span class="mf">0.3</span><span class="p">))</span> <span class="o">+</span> <span class="n">k</span><span class="o">*</span><span class="p">(</span><span class="n">cell</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">cell</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
<span class="c1"># Make box</span>
<span class="n">box</span> <span class="o">=</span> <span class="p">[</span><span class="n">p0</span><span class="p">,</span> <span class="n">v</span><span class="p">]</span>

<span class="c1"># initialize startgenerator (used to generate initial structures)</span>
<span class="n">sg</span> <span class="o">=</span> <span class="n">StartGenerator</span><span class="p">(</span><span class="n">template</span><span class="p">,</span> <span class="n">stoichiometry</span><span class="p">,</span> <span class="n">box</span><span class="p">)</span>

<span class="c1">### Set up candidate generation operations ###</span>
<span class="c1"># Set up constraint for rattle-mutation</span>
<span class="n">box_constraint</span> <span class="o">=</span> <span class="n">OperationConstraint</span><span class="p">(</span><span class="n">box</span><span class="o">=</span><span class="n">box</span><span class="p">)</span>

<span class="c1"># initialize rattle-mutation</span>
<span class="n">n_to_optimize</span> <span class="o">=</span> <span class="nb">len</span><span class="p">(</span><span class="n">stoichiometry</span><span class="p">)</span>
<span class="n">rattle</span> <span class="o">=</span> <span class="n">RattleMutation</span><span class="p">(</span><span class="n">n_to_optimize</span><span class="p">,</span> <span class="n">Nrattle</span><span class="o">=</span><span class="mi">2</span><span class="p">,</span> <span class="n">rattle_range</span><span class="o">=</span><span class="mi">4</span><span class="p">)</span>

<span class="n">candidate_generator</span> <span class="o">=</span> <span class="n">CandidateGenerator</span><span class="p">([</span><span class="mf">0.2</span><span class="p">,</span> <span class="mf">0.8</span><span class="p">],</span> <span class="p">[</span><span class="n">sg</span><span class="p">,</span> <span class="n">rattle</span><span class="p">])</span>

<span class="c1">### Initialize and run search ###</span>
<span class="n">search</span> <span class="o">=</span> <span class="n">GOFEE</span><span class="p">(</span><span class="n">calc</span><span class="o">=</span><span class="n">calc</span><span class="p">,</span>
               <span class="n">startgenerator</span><span class="o">=</span><span class="n">sg</span><span class="p">,</span>
               <span class="n">candidate_generator</span><span class="o">=</span><span class="n">candidate_generator</span><span class="p">,</span>
               <span class="n">max_steps</span><span class="o">=</span><span class="mi">150</span><span class="p">,</span>
               <span class="n">population_size</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span>
               <span class="n">position_constraint</span><span class="o">=</span><span class="n">box_constraint</span><span class="p">)</span>
<span class="n">search</span><span class="o">.</span><span class="n">run</span><span class="p">()</span>
</pre></div>
</div>
<p>If ASE and GPAW are set up and sourced propperly, you can run
the code as:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">mpiexec</span> <span class="o">--</span><span class="n">mca</span> <span class="n">mpi_warn_on_fork</span> <span class="mi">0</span> <span class="n">gpaw</span><span class="o">-</span><span class="n">python</span> <span class="n">Au7_on_Cu111</span><span class="o">.</span><span class="n">py</span>
</pre></div>
</div>
<p>What follows is a description of the elements of the python code
above, which relates to consraining the atomix position during
the search.</p>
<div class="section" id="box-setup">
<h2>Box setup<a class="headerlink" href="#box-setup" title="Permalink to this headline"></a></h2>
<p>As previously in the <a class="reference internal" href="../cu_clusters/cu_clusters.html#cu-cluster-search"><span class="std std-ref">Cu15 cluster search</span></a>,
we define a box in which initial atoms are placed. In this example we
will also use this box to constrain the position of the “free” atoms
during the search.
Defining a box positioned 0.3Å above the slab, with a height of 5Å and
with xy-dimensions shrunk, from all sides by a fraction “k”, relative
to the cell xy-dimensions, can be achieved by:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="c1">## Box for startgenerator and rattle-mutation</span>
<span class="n">k</span> <span class="o">=</span> <span class="mf">0.2</span>  <span class="c1"># Shrinkage fraction from each side of the box in v[0] and v[1] directions.</span>
<span class="n">cell</span> <span class="o">=</span> <span class="n">template</span><span class="o">.</span><span class="n">get_cell</span><span class="p">()</span>
<span class="c1"># Initialize box with cell</span>
<span class="n">v</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">copy</span><span class="p">(</span><span class="n">cell</span><span class="p">)</span>
<span class="c1"># Set height of box</span>
<span class="n">v</span><span class="p">[</span><span class="mi">2</span><span class="p">][</span><span class="mi">2</span><span class="p">]</span> <span class="o">=</span> <span class="mi">5</span>
<span class="c1"># Shrink box in v[0] and v[1] directions</span>
<span class="n">v</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span> <span class="o">*=</span> <span class="p">(</span><span class="mi">1</span><span class="o">-</span><span class="mi">2</span><span class="o">*</span><span class="n">k</span><span class="p">)</span>
<span class="n">v</span><span class="p">[</span><span class="mi">1</span><span class="p">]</span> <span class="o">*=</span> <span class="p">(</span><span class="mi">1</span><span class="o">-</span><span class="mi">2</span><span class="o">*</span><span class="n">k</span><span class="p">)</span>
<span class="c1"># Chose anker point p0 so box in centered in v[0] and v[1] directions.</span>
<span class="n">z_max_slab</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">max</span><span class="p">(</span><span class="n">template</span><span class="o">.</span><span class="n">get_positions</span><span class="p">()[:,</span><span class="mi">2</span><span class="p">])</span>
<span class="n">p0</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">((</span><span class="mi">0</span><span class="p">,</span> <span class="mi">0</span><span class="p">,</span> <span class="n">z_max_slab</span><span class="o">+</span><span class="mf">0.3</span><span class="p">))</span> <span class="o">+</span> <span class="n">k</span><span class="o">*</span><span class="p">(</span><span class="n">cell</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">+</span><span class="n">cell</span><span class="p">[</span><span class="mi">1</span><span class="p">])</span>
<span class="c1"># Make box</span>
<span class="n">box</span> <span class="o">=</span> <span class="p">[</span><span class="n">p0</span><span class="p">,</span> <span class="n">v</span><span class="p">]</span>
</pre></div>
</div>
</div>
<div class="section" id="constraint-object">
<h2>Constraint object<a class="headerlink" href="#constraint-object" title="Permalink to this headline"></a></h2>
<p>The constrraint object is made using:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">gofee.utils</span> <span class="k">import</span> <span class="n">OperationConstraint</span>
<span class="n">box_constraint</span> <span class="o">=</span> <span class="n">OperationConstraint</span><span class="p">(</span><span class="n">box</span><span class="o">=</span><span class="n">box</span><span class="p">)</span>
</pre></div>
</div>
</div>
<div class="section" id="initialize-constrained-gofee-search">
<h2>Initialize constrained GOFEE search<a class="headerlink" href="#initialize-constrained-gofee-search" title="Permalink to this headline"></a></h2>
<p>The constrained GOFEE search is initialized using the <code class="docutils literal notranslate"><span class="pre">position_constraint</span></code>
keyword:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span> <span class="nn">gofee</span> <span class="k">import</span> <span class="n">GOFEE</span>
<span class="n">search</span> <span class="o">=</span> <span class="n">GOFEE</span><span class="p">(</span><span class="n">calc</span><span class="o">=</span><span class="n">calc</span><span class="p">,</span>
            <span class="n">startgenerator</span><span class="o">=</span><span class="n">sg</span><span class="p">,</span>
            <span class="n">candidate_generator</span><span class="o">=</span><span class="n">candidate_generator</span><span class="p">,</span>
            <span class="n">max_steps</span><span class="o">=</span><span class="mi">150</span><span class="p">,</span>
            <span class="n">population_size</span><span class="o">=</span><span class="mi">5</span><span class="p">,</span>
            <span class="n">position_constraint</span><span class="o">=</span><span class="n">box_constraint</span><span class="p">)</span>
</pre></div>
</div>
</div>
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