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now we have a working documentation
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<li class="toctree-l4"><a class="reference internal" href="#grogupy.magnetism.blow_up_orbindx"><code class="docutils literal notranslate"><span class="pre">blow_up_orbindx()</span></code></a></li>
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<section id="module-grogupy.magnetism">
<span id="grogupy-magnetism-module"></span><h1>grogupy.magnetism module<a class="headerlink" href="#module-grogupy.magnetism" title="Link to this heading"></a></h1>
<dl class="py function">
<dt class="sig sig-object py" id="grogupy.magnetism.blow_up_orbindx">
<span class="sig-prename descclassname"><span class="pre">grogupy.magnetism.</span></span><span class="sig-name descname"><span class="pre">blow_up_orbindx</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">orb_indices</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/grogupy/magnetism.html#blow_up_orbindx"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#grogupy.magnetism.blow_up_orbindx" title="Link to this definition"></a></dt>
<dd><p>Function to blow up orbital indices to make SPIN BOX indices.</p>
<dl class="simple">
<dt>Args:</dt><dd><dl class="simple">
<dt>orb_indices<span class="classifier">np.array_like</span></dt><dd><p>These are the indices in ORBITAL BOX</p>
</dd>
</dl>
</dd>
<dt>Returns:</dt><dd><dl class="simple">
<dt>orb_indices<span class="classifier">np.array_like</span></dt><dd><p>These are the indices in SPIN BOX</p>
</dd>
</dl>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="grogupy.magnetism.calculate_anisotropy_tensor">
<span class="sig-prename descclassname"><span class="pre">grogupy.magnetism.</span></span><span class="sig-name descname"><span class="pre">calculate_anisotropy_tensor</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">mag_ent</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/grogupy/magnetism.html#calculate_anisotropy_tensor"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#grogupy.magnetism.calculate_anisotropy_tensor" title="Link to this definition"></a></dt>
<dd><p>Calculates the renormalized anisotropy tensor from the energies.</p>
<p>It uses the grogu convention for output.</p>
<dl class="simple">
<dt>Args:</dt><dd><dl class="simple">
<dt>mag_ent<span class="classifier">dict</span></dt><dd><p>An element from the magnetic entities</p>
</dd>
</dl>
</dd>
<dt>Returns:</dt><dd><dl class="simple">
<dt>K<span class="classifier">np.array_like</span></dt><dd><p>elements of the anisotropy tensor</p>
</dd>
</dl>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="grogupy.magnetism.calculate_exchange_tensor">
<span class="sig-prename descclassname"><span class="pre">grogupy.magnetism.</span></span><span class="sig-name descname"><span class="pre">calculate_exchange_tensor</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">pair</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/grogupy/magnetism.html#calculate_exchange_tensor"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#grogupy.magnetism.calculate_exchange_tensor" title="Link to this definition"></a></dt>
<dd><p>Calculates the exchange tensor from the energies.</p>
<p>It produces the isotropic exchange, the relevant elements
from the Dzyaloshinskii-Morilla (Dm) tensor, the symmetric-anisotropy
and the complete exchange tensor.</p>
<dl class="simple">
<dt>Args:</dt><dd><dl class="simple">
<dt>pair<span class="classifier">dict</span></dt><dd><p>An element from the pairs</p>
</dd>
</dl>
</dd>
<dt>Returns:</dt><dd><dl class="simple">
<dt>J_iso<span class="classifier">float</span></dt><dd><p>Isotropic exchange (Tr[J] / 3)</p>
</dd>
<dt>J_S<span class="classifier">np.array_like</span></dt><dd><p>Symmetric-anisotropy (J_S = J - J_iso * I ––&gt; Jxx, Jyy, Jxy, Jxz, Jyz)</p>
</dd>
<dt>D<span class="classifier">np.array_like</span></dt><dd><p>DM elements (Dx, Dy, Dz)</p>
</dd>
<dt>J<span class="classifier">np.array_like</span></dt><dd><p>Complete exchange tensor flattened (Jxx, Jxy, Jxz, Jyx, Jyy, Jyz, Jzx, Jzy, Jzz)</p>
</dd>
</dl>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="grogupy.magnetism.parse_magnetic_entity">
<span class="sig-prename descclassname"><span class="pre">grogupy.magnetism.</span></span><span class="sig-name descname"><span class="pre">parse_magnetic_entity</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">dh</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">atom</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="n"><span class="pre">l</span></span><span class="o"><span class="pre">=</span></span><span class="default_value"><span class="pre">None</span></span></em>, <em class="sig-param"><span class="o"><span class="pre">**</span></span><span class="n"><span class="pre">kwargs</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/grogupy/magnetism.html#parse_magnetic_entity"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#grogupy.magnetism.parse_magnetic_entity" title="Link to this definition"></a></dt>
<dd><p>Function to define orbital indexes of a given magnetic entity.</p>
<dl class="simple">
<dt>Args:</dt><dd><dl class="simple">
<dt>dh<span class="classifier">sisl.physics.Hamiltonian</span></dt><dd><p>Hamiltonian from sisl</p>
</dd>
<dt>atom<span class="classifier">integer or list of integers, optional</span></dt><dd><p>Defining atom (or atoms) in the unit cell forming the magnetic entity. Defaults to None</p>
</dd>
<dt>l<span class="classifier">integer, optional</span></dt><dd><p>Defining the angular momentum channel. Defaults to None</p>
</dd>
</dl>
</dd>
<dt>Returns:</dt><dd><dl class="simple">
<dt>list</dt><dd><p>The orbital indexes of the given magnetic entity</p>
</dd>
</dl>
</dd>
</dl>
</dd></dl>
<dl class="py function">
<dt class="sig sig-object py" id="grogupy.magnetism.spin_tracer">
<span class="sig-prename descclassname"><span class="pre">grogupy.magnetism.</span></span><span class="sig-name descname"><span class="pre">spin_tracer</span></span><span class="sig-paren">(</span><em class="sig-param"><span class="n"><span class="pre">M</span></span></em><span class="sig-paren">)</span><a class="reference internal" href="../_modules/grogupy/magnetism.html#spin_tracer"><span class="viewcode-link"><span class="pre">[source]</span></span></a><a class="headerlink" href="#grogupy.magnetism.spin_tracer" title="Link to this definition"></a></dt>
<dd><p>Spin tracer utility.</p>
<p>This takes an operator with the orbital-spin sequence:
orbital 1 up,
orbital 1 down,
orbital 2 up,
orbital 2 down,
that is in the SPIN-BOX representation,
and extracts orbital dependent Pauli traces.</p>
<dl class="simple">
<dt>Args:</dt><dd><dl class="simple">
<dt>M<span class="classifier">np.array_like</span></dt><dd><p>Traceable matrix</p>
</dd>
</dl>
</dd>
<dt>Returns:</dt><dd><dl class="simple">
<dt>dict</dt><dd><p>It contains the traced matrix with “x”, “y”, “z” and “c”</p>
</dd>
</dl>
</dd>
</dl>
</dd></dl>
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