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nanotheorygroup · Dec 4, 2024 · 81c248c · 81c248c
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diff --git a/_images/math/15cfbf59c2e9dda1f84c7dff795b1b1d95ca9bc1.png b/_images/math/15cfbf59c2e9dda1f84c7dff795b1b1d95ca9bc1.png
diff --git a/_modules/kaldo/conductivity.html b/_modules/kaldo/conductivity.html
@@ -553,7 +553,6 @@ <h1 id="modules-kaldo-conductivity--page-root">Source code for kaldo.conductivit
 <span class="sd">    Conductivity(phonons=phonons, method='inverse', storage='memory').conductivity.sum(axis=0))</span>
 <span class="sd">    ```</span>
 <span class="sd">    """</span>
-
     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">phonons</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">'phonons'</span><span class="p">)</span>
         <span class="bp">self</span><span class="o">.</span><span class="n">method</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">'method'</span><span class="p">,</span> <span class="s1">'rta'</span><span class="p">)</span>
@@ -584,7 +583,8 @@ <h1 id="modules-kaldo-conductivity--page-root">Source code for kaldo.conductivit
     <span class="nd">@lazy_property</span><span class="p">(</span>
         <span class="n">label</span><span class="o">=</span><span class="s1">'&lt;diffusivity_bandwidth&gt;/&lt;diffusivity_threshold&gt;/&lt;temperature&gt;/&lt;statistics&gt;/&lt;third_bandwidth&gt;/&lt;include_isotopes&gt;/&lt;method&gt;/&lt;length&gt;/&lt;finite_length_method&gt;'</span><span class="p">)</span>
     <span class="k">def</span> <span class="nf">conductivity</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-<span class="w">        </span><span class="sd">"""Calculate the thermal conductivity per mode in W/m/K</span>
+<span class="w">        </span><span class="sd">"""</span>
+<span class="sd">        Calculate the thermal conductivity per mode in W/m/K</span>
 
 <span class="sd">        Returns</span>
 <span class="sd">        -------</span>
@@ -622,7 +622,8 @@ <h1 id="modules-kaldo-conductivity--page-root">Source code for kaldo.conductivit
     <span class="nd">@lazy_property</span><span class="p">(</span>
         <span class="n">label</span><span class="o">=</span><span class="s1">'&lt;diffusivity_bandwidth&gt;/&lt;diffusivity_threshold&gt;/&lt;temperature&gt;/&lt;statistics&gt;/&lt;third_bandwidth&gt;/&lt;include_isotopes&gt;/&lt;method&gt;/&lt;length&gt;/&lt;finite_length_method&gt;'</span><span class="p">)</span>
     <span class="k">def</span> <span class="nf">mean_free_path</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-<span class="w">        </span><span class="sd">"""Calculate the mean_free_path per mode in A</span>
+<span class="w">        </span><span class="sd">"""</span>
+<span class="sd">        Calculate the mean_free_path per mode in A</span>
 
 <span class="sd">        Returns</span>
 <span class="sd">        -------</span>
@@ -652,7 +653,8 @@ <h1 id="modules-kaldo-conductivity--page-root">Source code for kaldo.conductivit
 
     <span class="nd">@property</span>
     <span class="k">def</span> <span class="nf">diffusivity</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-<span class="w">        </span><span class="sd">"""Calculate the diffusivity, for each k point in k_points and each mode.</span>
+<span class="w">        </span><span class="sd">"""</span>
+<span class="sd">        Calculate the diffusivity, for each k point in k_points and each mode.</span>
 
 <span class="sd">        Returns</span>
 <span class="sd">        -------</span>
@@ -784,7 +786,8 @@ <h1 id="modules-kaldo-conductivity--page-root">Source code for kaldo.conductivit
         <span class="k">return</span> <span class="n">conductivity_per_mode</span><span class="o">.</span><span class="n">reshape</span><span class="p">((</span><span class="bp">self</span><span class="o">.</span><span class="n">n_phonons</span><span class="p">,</span> <span class="mi">3</span><span class="p">,</span> <span class="mi">3</span><span class="p">))</span> <span class="o">*</span> <span class="mf">1e22</span><span class="p">,</span> <span class="n">diffusivity</span>
 
 <div class="viewcode-block" id="Conductivity.calculate_mfp_inverse"><a class="viewcode-back" href="../../docsource/api_conductivity.html#kaldo.conductivity.Conductivity.calculate_mfp_inverse">[docs]</a>    <span class="k">def</span> <span class="nf">calculate_mfp_inverse</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
-<span class="w">        </span><span class="sd">"""This method calculates the inverse of the mean free path for each phonon.</span>
+<span class="w">        </span><span class="sd">"""</span>
+<span class="sd">        This method calculates the inverse of the mean free path for each phonon.</span>
 <span class="sd">        The matrix returns k vectors for each mode and has units of inverse Angstroms.</span>
 
 <span class="sd">        Returns</span>
@@ -879,7 +882,8 @@ <h1 id="modules-kaldo-conductivity--page-root">Source code for kaldo.conductivit
             <span class="n">np</span><span class="o">.</span><span class="n">save</span><span class="p">(</span><span class="n">psi_inv_filename</span><span class="p">,</span> <span class="bp">self</span><span class="o">.</span><span class="n">_psi_inv</span><span class="p">)</span>
 
 <div class="viewcode-block" id="Conductivity.calculate_conductivity_full"><a class="viewcode-back" href="../../docsource/api_conductivity.html#kaldo.conductivity.Conductivity.calculate_conductivity_full">[docs]</a>    <span class="k">def</span> <span class="nf">calculate_conductivity_full</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">is_using_gamma_tensor_evects</span><span class="o">=</span><span class="kc">False</span><span class="p">):</span>
-<span class="w">        </span><span class="sd">"""This calculates the conductivity using the full solution of the space-dependent Boltzmann Transport Equation.</span>
+<span class="w">        </span><span class="sd">"""</span>
+<span class="sd">        This calculates the conductivity using the full solution of the space-dependent Boltzmann Transport Equation.</span>
 
 <span class="sd">        Returns</span>
 <span class="sd">        -------</span>

diff --git a/_modules/kaldo/forceconstants.html b/_modules/kaldo/forceconstants.html
@@ -469,7 +469,6 @@ <h1 id="modules-kaldo-forceconstants--page-root">Source code for kaldo.forcecons
 
 <span class="sd">    Parameters</span>
 <span class="sd">    ----------</span>
-
 <span class="sd">    atoms: Tabulated xyz files or ASE Atoms object</span>
 <span class="sd">        The atoms to work on.</span>
 <span class="sd">    supercell: (3) tuple, optional</span>
@@ -490,9 +489,7 @@ <h1 id="modules-kaldo-forceconstants--page-root">Source code for kaldo.forcecons
 
 <span class="sd">    Attributes</span>
 <span class="sd">    ----------</span>
-
 <span class="sd">    """</span>
-
     <span class="k">def</span> <span class="fm">__init__</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span>
                  <span class="n">atoms</span><span class="p">,</span>
                  <span class="n">supercell</span><span class="o">=</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="mi">1</span><span class="p">),</span>
@@ -569,7 +566,6 @@ <h1 id="modules-kaldo-forceconstants--page-root">Source code for kaldo.forcecons
 <span class="sd">            If true, the acoustic sum rule is applied to the dynamical matrix.</span>
 <span class="sd">            Default is False</span>
 
-
 <span class="sd">        Returns</span>
 <span class="sd">        -------</span>
 <span class="sd">        ForceConstants object</span>
@@ -597,14 +593,13 @@ <h1 id="modules-kaldo-forceconstants--page-root">Source code for kaldo.forcecons
         <span class="n">forceconstants</span><span class="o">.</span><span class="n">distance_threshold</span> <span class="o">=</span> <span class="n">distance_threshold</span>
         <span class="k">return</span> <span class="n">forceconstants</span></div>
 
-    <span class="k">def</span> <span class="nf">unfold_third_order</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">reduced_third</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">distance_threshold</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
+<div class="viewcode-block" id="ForceConstants.unfold_third_order"><a class="viewcode-back" href="../../docsource/api_forceconstants.html#kaldo.forceconstants.ForceConstants.unfold_third_order">[docs]</a>    <span class="k">def</span> <span class="nf">unfold_third_order</span><span class="p">(</span><span class="bp">self</span><span class="p">,</span> <span class="n">reduced_third</span><span class="o">=</span><span class="kc">None</span><span class="p">,</span> <span class="n">distance_threshold</span><span class="o">=</span><span class="kc">None</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">"""</span>
 <span class="sd">        This method extrapolates a third order force constant matrix from a unit</span>
 <span class="sd">        cell into a matrix for a larger supercell.</span>
 
 <span class="sd">        Parameters</span>
 <span class="sd">        ----------</span>
-
 <span class="sd">        reduced_third : array, optional</span>
 <span class="sd">            The third order force constant matrix.</span>
 <span class="sd">            Default is `self.third`</span>
@@ -661,10 +656,10 @@ <h1 id="modules-kaldo-forceconstants--page-root">Source code for kaldo.forcecons
         <span class="n">expanded_third</span> <span class="o">=</span> <span class="n">COO</span><span class="p">(</span><span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">coords</span><span class="p">)</span><span class="o">.</span><span class="n">T</span><span class="p">,</span> <span class="n">np</span><span class="o">.</span><span class="n">array</span><span class="p">(</span><span class="n">values</span><span class="p">),</span> <span class="n">shape</span><span class="p">)</span>
         <span class="n">expanded_third</span> <span class="o">=</span> <span class="n">expanded_third</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span>
             <span class="p">(</span><span class="n">n_unit_atoms</span> <span class="o">*</span> <span class="mi">3</span><span class="p">,</span> <span class="n">n_replicas</span> <span class="o">*</span> <span class="n">n_unit_atoms</span> <span class="o">*</span> <span class="mi">3</span><span class="p">,</span> <span class="n">n_replicas</span> <span class="o">*</span> <span class="n">n_unit_atoms</span> <span class="o">*</span> <span class="mi">3</span><span class="p">))</span>
-        <span class="k">return</span> <span class="n">expanded_third</span>
+        <span class="k">return</span> <span class="n">expanded_third</span></div>
 
 
-    <span class="k">def</span> <span class="nf">elastic_prop</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
+<div class="viewcode-block" id="ForceConstants.elastic_prop"><a class="viewcode-back" href="../../docsource/api_forceconstants.html#kaldo.forceconstants.ForceConstants.elastic_prop">[docs]</a>    <span class="k">def</span> <span class="nf">elastic_prop</span><span class="p">(</span><span class="bp">self</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">"""</span>
 <span class="sd">        Return the stiffness tensor (aka elastic modulus tensor) of the system in GPa. This describes the stress-strain</span>
 <span class="sd">        relationship of the material and can sometimes be used as a loose predictor for thermal conductivity. Requires</span>
@@ -678,6 +673,7 @@ <h1 id="modules-kaldo-forceconstants--page-root">Source code for kaldo.forcecons
 <span class="sd">        -------</span>
 <span class="sd">        C_ijkl : np.array(3, 3, 3, 3)</span>
 <span class="sd">            Elasticity tensor in GPa</span>
+
 <span class="sd">        """</span>
         <span class="c1"># Intake key parameters</span>
         <span class="n">atoms</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">atoms</span>
@@ -718,7 +714,7 @@ <h1 id="modules-kaldo-forceconstants--page-root">Source code for kaldo.forcecons
                         <span class="n">cijkl</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">,</span> <span class="n">k</span><span class="p">,</span> <span class="n">l</span><span class="p">]</span> <span class="o">=</span> <span class="n">b</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="n">k</span><span class="p">,</span> <span class="n">j</span><span class="p">,</span> <span class="n">l</span><span class="p">]</span> <span class="o">+</span> <span class="n">b</span><span class="p">[</span><span class="n">j</span><span class="p">,</span> <span class="n">k</span><span class="p">,</span> <span class="n">i</span><span class="p">,</span> <span class="n">l</span><span class="p">]</span> <span class="o">-</span> <span class="n">b</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">,</span> <span class="n">k</span><span class="p">,</span> <span class="n">l</span><span class="p">]</span> <span class="o">+</span> <span class="n">r</span><span class="p">[</span><span class="n">i</span><span class="p">,</span> <span class="n">j</span><span class="p">,</span> <span class="n">k</span><span class="p">,</span> <span class="n">l</span><span class="p">]</span>
 
         <span class="c1"># Denote parameter for irreducible Cij in the unit of GPa</span>
-        <span class="k">return</span> <span class="n">evperang3togpa</span> <span class="o">*</span> <span class="n">cijkl</span> <span class="o">/</span> <span class="n">evtotenjovermol</span>
+        <span class="k">return</span> <span class="n">evperang3togpa</span> <span class="o">*</span> <span class="n">cijkl</span> <span class="o">/</span> <span class="n">evtotenjovermol</span></div>
 
 
     <span class="nd">@staticmethod</span>
@@ -738,7 +734,7 @@ <h1 id="modules-kaldo-forceconstants--page-root">Source code for kaldo.forcecons
         <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">sqrt</span><span class="p">(</span><span class="n">mean_squared_error</span><span class="p">(</span><span class="n">md_forces</span><span class="p">,</span> <span class="n">harmonic_forces</span><span class="p">))</span> <span class="o">/</span> <span class="n">np</span><span class="o">.</span><span class="n">std</span><span class="p">(</span><span class="n">md_forces</span><span class="p">)</span>
 
 
-    <span class="nd">@staticmethod</span>
+<div class="viewcode-block" id="ForceConstants.sigma2_tdep_MD"><a class="viewcode-back" href="../../docsource/api_forceconstants.html#kaldo.forceconstants.ForceConstants.sigma2_tdep_MD">[docs]</a>    <span class="nd">@staticmethod</span>
     <span class="k">def</span> <span class="nf">sigma2_tdep_MD</span><span class="p">(</span><span class="n">fc_file</span><span class="o">=</span><span class="s1">'infile.forceconstant'</span><span class="p">,</span> <span class="n">primitive_file</span><span class="o">=</span><span class="s1">'infile.ucposcar'</span><span class="p">,</span>
                        <span class="n">supercell_file</span><span class="o">=</span><span class="s1">'infile.ssposcar'</span><span class="p">,</span> <span class="n">md_run</span><span class="o">=</span><span class="s1">'dump.xyz'</span><span class="p">):</span>
 <span class="w">        </span><span class="sd">"""</span>
@@ -759,6 +755,7 @@ <h1 id="modules-kaldo-forceconstants--page-root">Source code for kaldo.forcecons
 <span class="sd">        -------</span>
 <span class="sd">        float</span>
 <span class="sd">            The average sigma2 value.</span>
+
 <span class="sd">        """</span>
         <span class="n">initial_structure</span> <span class="o">=</span> <span class="n">read</span><span class="p">(</span><span class="n">supercell_file</span><span class="p">,</span> <span class="nb">format</span><span class="o">=</span><span class="s2">"vasp"</span><span class="p">)</span>
         <span class="n">second_order_fc</span> <span class="o">=</span> <span class="n">parse_tdep_forceconstant</span><span class="p">(</span>
@@ -774,7 +771,7 @@ <h1 id="modules-kaldo-forceconstants--page-root">Source code for kaldo.forcecons
         <span class="n">sigma_values</span> <span class="o">=</span> <span class="p">[</span><span class="n">ForceConstants</span><span class="o">.</span><span class="n">_calculate_sigma</span><span class="p">(</span><span class="n">atoms</span><span class="o">.</span><span class="n">get_forces</span><span class="p">(),</span> <span class="n">harm_force</span><span class="p">)</span>
                         <span class="k">for</span> <span class="n">atoms</span><span class="p">,</span> <span class="n">harm_force</span> <span class="ow">in</span> <span class="nb">zip</span><span class="p">(</span><span class="n">full_MD_traj</span><span class="p">,</span> <span class="n">force_harmonic</span><span class="p">)]</span>
 
-        <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">sigma_values</span><span class="p">)</span></div>
+        <span class="k">return</span> <span class="n">np</span><span class="o">.</span><span class="n">mean</span><span class="p">(</span><span class="n">sigma_values</span><span class="p">)</span></div></div>
 
 </pre></div>