deploy: 01320fa

mala-project · Nov 21, 2024 · de17536 · de17536
1 parent 0139675
commit de17536
Show file tree

Hide file tree

Showing 13 changed files with 123 additions and 94 deletions.
diff --git a/_modules/mala/common/parameters.html b/_modules/mala/common/parameters.html
diff --git a/_modules/mala/network/hyper_opt_oat.html b/_modules/mala/network/hyper_opt_oat.html
@@ -518,12 +518,6 @@ <h1>Source code for mala.network.hyper_opt_oat</h1><div class="highlight"><pre>
 
             <span class="bp">self</span><span class="o">.</span><span class="n">_save_params_and_scaler</span><span class="p">()</span>
 
-            <span class="c1"># Next, we save all the other objects.</span>
-            <span class="c1"># Here some horovod stuff would have to go.</span>
-            <span class="c1"># But so far, the optuna implementation is not horovod-ready...</span>
-            <span class="c1"># if self.params.use_horovod:</span>
-            <span class="c1">#     if hvd.rank() != 0:</span>
-            <span class="c1">#         return</span>
             <span class="c1"># The study only has to be saved if the no RDB storage is used.</span>
             <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="o">.</span><span class="n">hyperparameters</span><span class="o">.</span><span class="n">rdb_storage</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
                 <span class="n">hyperopt_name</span> <span class="o">=</span> <span class="p">(</span>

diff --git a/_modules/mala/network/hyper_opt_optuna.html b/_modules/mala/network/hyper_opt_optuna.html
@@ -487,12 +487,6 @@ <h1>Source code for mala.network.hyper_opt_optuna</h1><div class="highlight"><pr
 
             <span class="bp">self</span><span class="o">.</span><span class="n">_save_params_and_scaler</span><span class="p">()</span>
 
-            <span class="c1"># Next, we save all the other objects.</span>
-            <span class="c1"># Here some horovod stuff would have to go.</span>
-            <span class="c1"># But so far, the optuna implementation is not horovod-ready...</span>
-            <span class="c1"># if self.params.use_horovod:</span>
-            <span class="c1">#     if hvd.rank() != 0:</span>
-            <span class="c1">#         return</span>
             <span class="c1"># The study only has to be saved if the no RDB storage is used.</span>
             <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">params</span><span class="o">.</span><span class="n">hyperparameters</span><span class="o">.</span><span class="n">rdb_storage</span> <span class="ow">is</span> <span class="kc">None</span><span class="p">:</span>
                 <span class="n">hyperopt_name</span> <span class="o">=</span> <span class="p">(</span>

diff --git a/_modules/mala/targets/density.html b/_modules/mala/targets/density.html
@@ -1266,7 +1266,7 @@ <h1>Source code for mala.targets.density</h1><div class="highlight"><pre>
         <span class="c1"># instantiate the process with the file.</span>
         <span class="n">positions_for_qe</span> <span class="o">=</span> <span class="bp">self</span><span class="o">.</span><span class="n">get_scaled_positions_for_qe</span><span class="p">(</span><span class="n">atoms_Angstrom</span><span class="p">)</span>
 
-        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_parameters_full</span><span class="o">.</span><span class="n">descriptors</span><span class="o">.</span><span class="n">use_atomic_density_energy_formula</span><span class="p">:</span>
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">parameters</span><span class="o">.</span><span class="n">_configuration</span><span class="p">[</span><span class="s2">&quot;atomic_density_formula&quot;</span><span class="p">]:</span>
             <span class="c1"># Calculate the Gaussian descriptors for the calculation of the</span>
             <span class="c1"># structure factors.</span>
             <span class="n">barrier</span><span class="p">()</span>
@@ -1335,8 +1335,8 @@ <h1>Source code for mala.targets.density</h1><div class="highlight"><pre>
         <span class="n">te</span><span class="o">.</span><span class="n">set_positions</span><span class="p">(</span>
             <span class="n">np</span><span class="o">.</span><span class="n">transpose</span><span class="p">(</span><span class="n">positions_for_qe</span><span class="p">),</span>
             <span class="n">number_of_atoms</span><span class="p">,</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">_parameters_full</span><span class="o">.</span><span class="n">descriptors</span><span class="o">.</span><span class="n">use_atomic_density_energy_formula</span><span class="p">,</span>
-            <span class="bp">self</span><span class="o">.</span><span class="n">_parameters_full</span><span class="o">.</span><span class="n">descriptors</span><span class="o">.</span><span class="n">use_atomic_density_energy_formula</span><span class="p">,</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">parameters</span><span class="o">.</span><span class="n">_configuration</span><span class="p">[</span><span class="s2">&quot;atomic_density_formula&quot;</span><span class="p">],</span>
+            <span class="bp">self</span><span class="o">.</span><span class="n">parameters</span><span class="o">.</span><span class="n">_configuration</span><span class="p">[</span><span class="s2">&quot;atomic_density_formula&quot;</span><span class="p">],</span>
         <span class="p">)</span>
         <span class="n">barrier</span><span class="p">()</span>
         <span class="n">printout</span><span class="p">(</span>
@@ -1347,7 +1347,7 @@ <h1>Source code for mala.targets.density</h1><div class="highlight"><pre>
         <span class="p">)</span>
         <span class="n">barrier</span><span class="p">()</span>
 
-        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">_parameters_full</span><span class="o">.</span><span class="n">descriptors</span><span class="o">.</span><span class="n">use_atomic_density_energy_formula</span><span class="p">:</span>
+        <span class="k">if</span> <span class="bp">self</span><span class="o">.</span><span class="n">parameters</span><span class="o">.</span><span class="n">_configuration</span><span class="p">[</span><span class="s2">&quot;atomic_density_formula&quot;</span><span class="p">]:</span>
             <span class="n">t0</span> <span class="o">=</span> <span class="n">time</span><span class="o">.</span><span class="n">perf_counter</span><span class="p">()</span>
             <span class="n">gaussian_descriptors</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span>
                 <span class="n">gaussian_descriptors</span><span class="p">,</span>

diff --git a/_sources/advanced_usage/predictions.rst.txt b/_sources/advanced_usage/predictions.rst.txt
@@ -81,11 +81,13 @@ Gaussian representation of atomic positions. In this algorithm, most of the
 computational overhead of the total energy calculation is offloaded to the
 computation of this Gaussian representation. This calculation is realized via
 LAMMPS and can therefore be GPU accelerated (parallelized) in the same fashion
-as the bispectrum descriptor calculation. Simply activate this option via
+as the bispectrum descriptor calculation. If a GPU is activated (and LAMMPS
+is available), this option will be used by default. It can also manually be
+activated via
 
     .. code-block:: python
 
-        parameters.descriptors.use_atomic_density_energy_formula = True
+        parameters.use_atomic_density_formula = True
 
 The Gaussian representation algorithm is describe in
 the publication `Predicting electronic structures at any length scale with machine learning <doi.org/10.1038/s41524-023-01070-z>`_.

diff --git a/advanced_usage/predictions.html b/advanced_usage/predictions.html
@@ -168,9 +168,11 @@
 computational overhead of the total energy calculation is offloaded to the
 computation of this Gaussian representation. This calculation is realized via
 LAMMPS and can therefore be GPU accelerated (parallelized) in the same fashion
-as the bispectrum descriptor calculation. Simply activate this option via</p>
+as the bispectrum descriptor calculation. If a GPU is activated (and LAMMPS
+is available), this option will be used by default. It can also manually be
+activated via</p>
 <blockquote>
-<div><div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">parameters</span><span class="o">.</span><span class="n">descriptors</span><span class="o">.</span><span class="n">use_atomic_density_energy_formula</span> <span class="o">=</span> <span class="kc">True</span>
+<div><div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="n">parameters</span><span class="o">.</span><span class="n">use_atomic_density_formula</span> <span class="o">=</span> <span class="kc">True</span>
 </pre></div>
 </div>
 </div></blockquote>

diff --git a/api/mala.common.html b/api/mala.common.html
@@ -146,7 +146,6 @@ <h1>common<a class="headerlink" href="#common" title="Link to this heading"><
 <li class="toctree-l3"><a class="reference internal" href="mala.common.parameters.html#mala.common.parameters.Parameters.data"><code class="docutils literal notranslate"><span class="pre">Parameters.data</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="mala.common.parameters.html#mala.common.parameters.Parameters.running"><code class="docutils literal notranslate"><span class="pre">Parameters.running</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="mala.common.parameters.html#mala.common.parameters.Parameters.hyperparameters"><code class="docutils literal notranslate"><span class="pre">Parameters.hyperparameters</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="mala.common.parameters.html#mala.common.parameters.Parameters.debug"><code class="docutils literal notranslate"><span class="pre">Parameters.debug</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="mala.common.parameters.html#mala.common.parameters.Parameters.manual_seed"><code class="docutils literal notranslate"><span class="pre">Parameters.manual_seed</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="mala.common.parameters.html#mala.common.parameters.Parameters.load_from_file"><code class="docutils literal notranslate"><span class="pre">Parameters.load_from_file()</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="mala.common.parameters.html#mala.common.parameters.Parameters.load_from_json"><code class="docutils literal notranslate"><span class="pre">Parameters.load_from_json()</span></code></a></li>
@@ -159,6 +158,7 @@ <h1>common<a class="headerlink" href="#common" title="Link to this heading"><
 <li class="toctree-l3"><a class="reference internal" href="mala.common.parameters.html#mala.common.parameters.Parameters.device"><code class="docutils literal notranslate"><span class="pre">Parameters.device</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="mala.common.parameters.html#mala.common.parameters.Parameters.openpmd_configuration"><code class="docutils literal notranslate"><span class="pre">Parameters.openpmd_configuration</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="mala.common.parameters.html#mala.common.parameters.Parameters.openpmd_granularity"><code class="docutils literal notranslate"><span class="pre">Parameters.openpmd_granularity</span></code></a></li>
+<li class="toctree-l3"><a class="reference internal" href="mala.common.parameters.html#mala.common.parameters.Parameters.use_atomic_density_formula"><code class="docutils literal notranslate"><span class="pre">Parameters.use_atomic_density_formula</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="mala.common.parameters.html#mala.common.parameters.Parameters.use_ddp"><code class="docutils literal notranslate"><span class="pre">Parameters.use_ddp</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="mala.common.parameters.html#mala.common.parameters.Parameters.use_gpu"><code class="docutils literal notranslate"><span class="pre">Parameters.use_gpu</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="mala.common.parameters.html#mala.common.parameters.Parameters.use_lammps"><code class="docutils literal notranslate"><span class="pre">Parameters.use_lammps</span></code></a></li>
@@ -173,7 +173,6 @@ <h1>common<a class="headerlink" href="#common" title="Link to this heading"><
 </ul>
 </li>
 <li class="toctree-l2"><a class="reference internal" href="mala.common.parameters.html#mala.common.parameters.ParametersData"><code class="docutils literal notranslate"><span class="pre">ParametersData</span></code></a><ul>
-<li class="toctree-l3"><a class="reference internal" href="mala.common.parameters.html#mala.common.parameters.ParametersData.descriptors_contain_xyz"><code class="docutils literal notranslate"><span class="pre">ParametersData.descriptors_contain_xyz</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="mala.common.parameters.html#mala.common.parameters.ParametersData.snapshot_directories_list"><code class="docutils literal notranslate"><span class="pre">ParametersData.snapshot_directories_list</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="mala.common.parameters.html#mala.common.parameters.ParametersData.data_splitting_type"><code class="docutils literal notranslate"><span class="pre">ParametersData.data_splitting_type</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="mala.common.parameters.html#mala.common.parameters.ParametersData.input_rescaling_type"><code class="docutils literal notranslate"><span class="pre">ParametersData.input_rescaling_type</span></code></a></li>
@@ -205,7 +204,6 @@ <h1>common<a class="headerlink" href="#common" title="Link to this heading"><
 <li class="toctree-l3"><a class="reference internal" href="mala.common.parameters.html#mala.common.parameters.ParametersDescriptors.lammps_compute_file"><code class="docutils literal notranslate"><span class="pre">ParametersDescriptors.lammps_compute_file</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="mala.common.parameters.html#mala.common.parameters.ParametersDescriptors.descriptors_contain_xyz"><code class="docutils literal notranslate"><span class="pre">ParametersDescriptors.descriptors_contain_xyz</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="mala.common.parameters.html#mala.common.parameters.ParametersDescriptors.atomic_density_sigma"><code class="docutils literal notranslate"><span class="pre">ParametersDescriptors.atomic_density_sigma</span></code></a></li>
-<li class="toctree-l3"><a class="reference internal" href="mala.common.parameters.html#mala.common.parameters.ParametersDescriptors.use_atomic_density_energy_formula"><code class="docutils literal notranslate"><span class="pre">ParametersDescriptors.use_atomic_density_energy_formula</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="mala.common.parameters.html#mala.common.parameters.ParametersDescriptors.bispectrum_cutoff"><code class="docutils literal notranslate"><span class="pre">ParametersDescriptors.bispectrum_cutoff</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="mala.common.parameters.html#mala.common.parameters.ParametersDescriptors.bispectrum_switchflag"><code class="docutils literal notranslate"><span class="pre">ParametersDescriptors.bispectrum_switchflag</span></code></a></li>
 <li class="toctree-l3"><a class="reference internal" href="mala.common.parameters.html#mala.common.parameters.ParametersDescriptors.use_y_splitting"><code class="docutils literal notranslate"><span class="pre">ParametersDescriptors.use_y_splitting</span></code></a></li>