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| <h1>Source code for mlcalcdriver.interfaces.ase_interface</h1><div class="highlight"><pre> | ||
| <span></span><span class="kn">import</span> <span class="nn">ase</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">mlcalcdriver.base</span> <span class="k">import</span> <span class="n">Posinp</span> | ||
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| <div class="viewcode-block" id="posinp_to_ase_atoms"><a class="viewcode-back" href="../../../ase_interface.html#mlcalcdriver.interfaces.ase_interface.posinp_to_ase_atoms">[docs]</a><span class="k">def</span> <span class="nf">posinp_to_ase_atoms</span><span class="p">(</span><span class="n">posinp</span><span class="p">):</span> | ||
| <span class="sa">r</span><span class="sd">"""</span> | ||
| <span class="sd"> Converts a :class:`Posinp` instance to an :class:`ase.Atoms`</span> | ||
| <span class="sd"> instance.</span> | ||
| <span class="sd"> """</span> | ||
| <span class="n">symbols</span><span class="p">,</span> <span class="n">positions</span><span class="p">,</span> <span class="n">masses</span> <span class="o">=</span> <span class="s2">""</span><span class="p">,</span> <span class="p">[],</span> <span class="p">[]</span> | ||
| <span class="k">for</span> <span class="n">atom</span> <span class="ow">in</span> <span class="n">posinp</span><span class="o">.</span><span class="n">atoms</span><span class="p">:</span> | ||
| <span class="n">symbols</span> <span class="o">+=</span> <span class="n">atom</span><span class="o">.</span><span class="n">type</span> | ||
| <span class="n">positions</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">atom</span><span class="o">.</span><span class="n">position</span><span class="p">)</span> | ||
| <span class="n">masses</span><span class="o">.</span><span class="n">append</span><span class="p">(</span><span class="n">atom</span><span class="o">.</span><span class="n">mass</span><span class="p">)</span> | ||
| <span class="k">if</span> <span class="n">posinp</span><span class="o">.</span><span class="n">boundary_conditions</span> <span class="o">==</span> <span class="s2">"free"</span><span class="p">:</span> | ||
| <span class="n">pbc</span> <span class="o">=</span> <span class="kc">False</span> | ||
| <span class="k">elif</span> <span class="n">posinp</span><span class="o">.</span><span class="n">boundary_conditions</span> <span class="o">==</span> <span class="s2">"surface"</span><span class="p">:</span> | ||
| <span class="n">pbc</span> <span class="o">=</span> <span class="p">(</span><span class="kc">True</span><span class="p">,</span> <span class="kc">False</span><span class="p">,</span> <span class="kc">True</span><span class="p">)</span> | ||
| <span class="k">elif</span> <span class="n">posinp</span><span class="o">.</span><span class="n">boundary_conditions</span> <span class="o">==</span> <span class="s2">"periodic"</span><span class="p">:</span> | ||
| <span class="n">pbc</span> <span class="o">=</span> <span class="kc">True</span> | ||
| <span class="n">atoms</span> <span class="o">=</span> <span class="n">ase</span><span class="o">.</span><span class="n">Atoms</span><span class="p">(</span> | ||
| <span class="n">symbols</span><span class="o">=</span><span class="n">symbols</span><span class="p">,</span> <span class="n">positions</span><span class="o">=</span><span class="n">positions</span><span class="p">,</span> <span class="n">masses</span><span class="o">=</span><span class="n">masses</span><span class="p">,</span> <span class="n">cell</span><span class="o">=</span><span class="n">posinp</span><span class="o">.</span><span class="n">cell</span><span class="p">,</span> <span class="n">pbc</span><span class="o">=</span><span class="n">pbc</span> | ||
| <span class="p">)</span> | ||
| <span class="k">return</span> <span class="n">atoms</span></div> | ||
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| <div class="viewcode-block" id="ase_atoms_to_posinp"><a class="viewcode-back" href="../../../ase_interface.html#mlcalcdriver.interfaces.ase_interface.ase_atoms_to_posinp">[docs]</a><span class="k">def</span> <span class="nf">ase_atoms_to_posinp</span><span class="p">(</span><span class="n">atoms</span><span class="p">):</span> | ||
| <span class="sa">r</span><span class="sd">"""</span> | ||
| <span class="sd"> Converts an :class:`ase.Atoms` instance to a</span> | ||
| <span class="sd"> :class:`Posinp` instance.</span> | ||
| <span class="sd"> """</span> | ||
| <span class="n">pos_dict</span> <span class="o">=</span> <span class="p">{</span><span class="s2">"units"</span><span class="p">:</span> <span class="s2">"angstroem"</span><span class="p">}</span> | ||
| <span class="n">positions</span> <span class="o">=</span> <span class="p">[]</span> | ||
| <span class="k">for</span> <span class="n">at</span> <span class="ow">in</span> <span class="n">atoms</span><span class="p">:</span> | ||
| <span class="n">positions</span><span class="o">.</span><span class="n">append</span><span class="p">({</span><span class="n">at</span><span class="o">.</span><span class="n">symbol</span><span class="p">:</span> <span class="n">at</span><span class="o">.</span><span class="n">position</span><span class="p">})</span> | ||
| <span class="n">cell</span> <span class="o">=</span> <span class="n">atoms</span><span class="o">.</span><span class="n">get_cell</span><span class="p">()</span> | ||
| <span class="k">if</span> <span class="n">cell</span><span class="o">.</span><span class="n">orthorhombic</span><span class="p">:</span> | ||
| <span class="k">if</span> <span class="p">(</span><span class="n">cell</span><span class="o">==</span><span class="mf">0.0</span><span class="p">)</span><span class="o">.</span><span class="n">all</span><span class="p">():</span> | ||
| <span class="n">new_cell</span> <span class="o">=</span> <span class="kc">None</span> | ||
| <span class="k">elif</span> <span class="n">cell</span><span class="p">[</span><span class="mi">1</span><span class="p">,</span><span class="mi">1</span><span class="p">]</span> <span class="ow">in</span> <span class="p">[</span><span class="mf">0.0</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">inf</span><span class="p">]:</span> | ||
| <span class="n">new_cell</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="mi">0</span><span class="p">],</span> <span class="nb">str</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">inf</span><span class="p">),</span> <span class="n">cell</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="k">else</span><span class="p">:</span> | ||
| <span class="n">new_cell</span> <span class="o">=</span> <span class="p">[</span><span class="n">dim</span><span class="p">[</span><span class="n">i</span><span class="p">]</span> <span class="k">for</span> <span class="n">i</span><span class="p">,</span> <span class="n">dim</span> <span class="ow">in</span> <span class="nb">enumerate</span><span class="p">(</span><span class="n">cell</span><span class="p">)]</span> | ||
| <span class="k">else</span><span class="p">:</span> | ||
| <span class="k">raise</span> <span class="ne">NotImplementedError</span><span class="p">(</span><span class="s2">"Non orthorhombic cells are not supported yet."</span><span class="p">)</span> | ||
| <span class="n">pos_dict</span><span class="p">[</span><span class="s2">"positions"</span><span class="p">]</span> <span class="o">=</span> <span class="n">positions</span> | ||
| <span class="n">pos_dict</span><span class="p">[</span><span class="s2">"cell"</span><span class="p">]</span> <span class="o">=</span> <span class="n">new_cell</span> | ||
| <span class="k">return</span> <span class="n">Posinp</span><span class="o">.</span><span class="n">from_dict</span><span class="p">(</span><span class="n">pos_dict</span><span class="p">)</span></div> | ||
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