build based on b609614

previews/PR246/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.5","generation_timestamp":"2024-09-11T05:30:20","documenter_version":"1.7.0"}}
+{"documenter":{"julia_version":"1.10.5","generation_timestamp":"2024-09-11T18:50:56","documenter_version":"1.7.0"}}

previews/PR246/gettingstarted/aceintro/index.html

@@ -6,4 +6,4 @@
    \sum_j \phi_{nlm}({\bm r}_j).\]</p><h3 id="Density-correlations"><a class="docs-heading-anchor" href="#Density-correlations">Density correlations</a><a id="Density-correlations-1"></a><a class="docs-heading-anchor-permalink" href="#Density-correlations" title="Permalink"></a></h3><p>Next, we form the <span>$N$</span>-correlations of the density, <span>$\rho^{\otimes N}$</span> and project them onto the tensor project basis, </p><p class="math-container">\[   {\bm A}_{\mathbf{nlm}}
    = \Big\langle \otimes_{t = 1}^N \phi_{n_t l_t m_t}, \rho^{\otimes N} \Big\rangle 
    = \prod_{t = 1}^N A_{n_t l_t m_t}.\]</p><p>The reason to introduce these is that in the next step, the symmetrisation step, the density project would lose all angular information while the <span>$N$</span>-correlations retain most (though not all) of it. </p><h3 id="Symmetrisation"><a class="docs-heading-anchor" href="#Symmetrisation">Symmetrisation</a><a id="Symmetrisation-1"></a><a class="docs-heading-anchor-permalink" href="#Symmetrisation" title="Permalink"></a></h3><p>Finally, we symmetrise the <span>$N$</span>-correlations, by integrating over the <span>$O(3)$</span>-Haar measure, </p><p class="math-container">\[  B_{\mathbf{nlm}} \propto 
-  \int_{O(3)} {\bm A}_{\mathbf{nlm}} \circ Q \, dQ \]</p><p>Because of properties of the spherical harmonics one can write this as </p><p class="math-container">\[  {\bm B} = \mathcal{U} {\bm A},\]</p><p>where <span>${\bm A}$</span> is the vector of 1, 2, ..., N correlations (the maximal <span>$N$</span> is an approximation parameter!) and <span>$\mathcal{U}$</span> is a sparse matrix (the coupling coefficients).</p><p>If one symmetrised all possible <span>$N$</span>-correlations then this would create a spanning set, but one can easily reduce this to an actual basis. This construction then yields a basis of the space of symmetric polynomials. </p><p>Notes: </p><ul><li>Because of permutation symmetry only ordered <span>${\bm v}$</span> tuples are retained</li></ul><h3 id="Linear-Dependence"><a class="docs-heading-anchor" href="#Linear-Dependence">Linear Dependence</a><a id="Linear-Dependence-1"></a><a class="docs-heading-anchor-permalink" href="#Linear-Dependence" title="Permalink"></a></h3><p>The construction described above introduces a lot of linear dependence which is removed in the ACE basis construction in a mixed symbolic / numerical procedure. In the end we no longer index the symmetrized basis functions as <span>$B_{\bm nlm}$</span> but as <span>$B_{\mathbf{nl}i}$</span> with <span>$i$</span> indexing the linearly independent basis functions from the <span>$\mathbf{nl}$</span> block. </p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../parallel-fitting/">« Parallel Fitting</a><a class="docs-footer-nextpage" href="../pkg/">Using the Julia Package Manager »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.7.0 on <span class="colophon-date" title="Wednesday 11 September 2024 05:30">Wednesday 11 September 2024</span>. Using Julia version 1.10.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+  \int_{O(3)} {\bm A}_{\mathbf{nlm}} \circ Q \, dQ \]</p><p>Because of properties of the spherical harmonics one can write this as </p><p class="math-container">\[  {\bm B} = \mathcal{U} {\bm A},\]</p><p>where <span>${\bm A}$</span> is the vector of 1, 2, ..., N correlations (the maximal <span>$N$</span> is an approximation parameter!) and <span>$\mathcal{U}$</span> is a sparse matrix (the coupling coefficients).</p><p>If one symmetrised all possible <span>$N$</span>-correlations then this would create a spanning set, but one can easily reduce this to an actual basis. This construction then yields a basis of the space of symmetric polynomials. </p><p>Notes: </p><ul><li>Because of permutation symmetry only ordered <span>${\bm v}$</span> tuples are retained</li></ul><h3 id="Linear-Dependence"><a class="docs-heading-anchor" href="#Linear-Dependence">Linear Dependence</a><a id="Linear-Dependence-1"></a><a class="docs-heading-anchor-permalink" href="#Linear-Dependence" title="Permalink"></a></h3><p>The construction described above introduces a lot of linear dependence which is removed in the ACE basis construction in a mixed symbolic / numerical procedure. In the end we no longer index the symmetrized basis functions as <span>$B_{\bm nlm}$</span> but as <span>$B_{\mathbf{nl}i}$</span> with <span>$i$</span> indexing the linearly independent basis functions from the <span>$\mathbf{nl}$</span> block. </p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../parallel-fitting/">« Parallel Fitting</a><a class="docs-footer-nextpage" href="../pkg/">Using the Julia Package Manager »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.7.0 on <span class="colophon-date" title="Wednesday 11 September 2024 18:50">Wednesday 11 September 2024</span>. Using Julia version 1.10.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

previews/PR246/gettingstarted/installation/index.html

@@ -8,4 +8,4 @@
 registry add https://github.com/ACEsuit/ACEregistry</code></pre><p>Press Backspace or <code>Ctrl-c</code> to exit the package manager. Use <code>Ctrl-d</code>, or <code>exit()</code> followed by Enter, to close the Julia REPL.</p><h4 id="Setting-up-a-new-ACEpotentials.jl-project"><a class="docs-heading-anchor" href="#Setting-up-a-new-ACEpotentials.jl-project">Setting up a new <code>ACEpotentials.jl</code> project</a><a id="Setting-up-a-new-ACEpotentials.jl-project-1"></a><a class="docs-heading-anchor-permalink" href="#Setting-up-a-new-ACEpotentials.jl-project" title="Permalink"></a></h4><p>Create a folder for your new project and change to it. Start the Julia REPL and activate a new project by switching to the package manager with <code>]</code>, and then running</p><pre><code class="language-julia hljs">activate .</code></pre><p>Now you can install <code>ACEpotentials</code>. Remaining in the package manager, use</p><pre><code class="language-julia hljs">add ACEpotentials</code></pre><p>Depending on your usage you may also need to add other packages, e.g. <code>AtomsBase</code>, <code>Molly</code>, <code>DFTK</code> etc.</p><h4 id="Returning-to-a-project"><a class="docs-heading-anchor" href="#Returning-to-a-project">Returning to a project</a><a id="Returning-to-a-project-1"></a><a class="docs-heading-anchor-permalink" href="#Returning-to-a-project" title="Permalink"></a></h4><p>When returning to a project, there are several methods for reactivating it. One is to simply <code>activate .</code> in the package manager, as above. Alternatively set the <code>JULIA_PROJECT</code> environment variable to the directory with <code>Project.toml</code> before starting julia, or call julia as <code>julia --project=&lt;dir&gt;</code>. Special syntax like <code>JULIA_PROJECT=@.</code> or <code>julia --project=@.</code> searches the current directory and its parents for a <code>Project.toml</code> file.</p><h3 id="Setting-up-the-Python-ASE-calculator"><a class="docs-heading-anchor" href="#Setting-up-the-Python-ASE-calculator">Setting up the Python ASE calculator</a><a id="Setting-up-the-Python-ASE-calculator-1"></a><a class="docs-heading-anchor-permalink" href="#Setting-up-the-Python-ASE-calculator" title="Permalink"></a></h3><div class="admonition is-warning"><header class="admonition-header">Warning</header><div class="admonition-body"><p>The current version of ACEpotentials does not have a tested ASE interface. If you need an ASE interface, consider using a version  &lt; 0.8 of ACEpotentials.</p></div></div><p>We use a wrapper called <code>pyjulip</code> to call julia and evaluate ACE potentials. In a terminal, with the correct julia project and python environment selected, run the following code:</p><pre><code class="nohighlight hljs">python -m pip install julia
 python -c &quot;import julia; julia.install()&quot;</code></pre><p>Make sure to use the correct python and pip, e.g. the ones that are in the correct Conda environment. Then, to set up <code>pyjulip</code>:</p><pre><code class="nohighlight hljs">git clone https://github.com/casv2/pyjulip.git
 cd pyjulip
-pip install .</code></pre><h3 id="Troubleshooting"><a class="docs-heading-anchor" href="#Troubleshooting">Troubleshooting</a><a id="Troubleshooting-1"></a><a class="docs-heading-anchor-permalink" href="#Troubleshooting" title="Permalink"></a></h3><p>There are currently no known recurring problems with <code>ACEpotentials</code> installation.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../">« Home</a><a class="docs-footer-nextpage" href="../saving-and-loading/">Saving and Loading Potentials »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.7.0 on <span class="colophon-date" title="Wednesday 11 September 2024 05:30">Wednesday 11 September 2024</span>. Using Julia version 1.10.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+pip install .</code></pre><h3 id="Troubleshooting"><a class="docs-heading-anchor" href="#Troubleshooting">Troubleshooting</a><a id="Troubleshooting-1"></a><a class="docs-heading-anchor-permalink" href="#Troubleshooting" title="Permalink"></a></h3><p>There are currently no known recurring problems with <code>ACEpotentials</code> installation.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../">« Home</a><a class="docs-footer-nextpage" href="../saving-and-loading/">Saving and Loading Potentials »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.7.0 on <span class="colophon-date" title="Wednesday 11 September 2024 18:50">Wednesday 11 September 2024</span>. Using Julia version 1.10.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

previews/PR246/gettingstarted/parallel-fitting/index.html

@@ -5,4 +5,4 @@
 @everywhere using ACEpotentials</code></pre><h3 id="Parallel-BLAS-or-LAPACK"><a class="docs-heading-anchor" href="#Parallel-BLAS-or-LAPACK">Parallel <code>BLAS</code> or <code>LAPACK</code></a><a id="Parallel-BLAS-or-LAPACK-1"></a><a class="docs-heading-anchor-permalink" href="#Parallel-BLAS-or-LAPACK" title="Permalink"></a></h3><p>Many <code>ACEfit</code> solvers, and possibly other routines, utilize <code>BLAS</code> or <code>LAPACK</code>. To see benefits from threading, one should set one or more of the following environment variables, depending on the particular library used.</p><pre><code class="language-bash hljs">export OMP_NUM_THREADS=8
 export MKL_NUM_THREADS=8
 export OPENBLAS_NUM_THREADS=8
-export VECLIB_MAXIMUM_THREADS=8</code></pre><p>Distributed solution of the linear least squares systems is currently not supported. We would welcome collaboration on this with interested developers. </p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../tutorials/scripting/">« Basic Shell Workflow</a><a class="docs-footer-nextpage" href="../aceintro/">Introduction to ACE Models »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.7.0 on <span class="colophon-date" title="Wednesday 11 September 2024 05:30">Wednesday 11 September 2024</span>. Using Julia version 1.10.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+export VECLIB_MAXIMUM_THREADS=8</code></pre><p>Distributed solution of the linear least squares systems is currently not supported. We would welcome collaboration on this with interested developers. </p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../../tutorials/scripting/">« Basic Shell Workflow</a><a class="docs-footer-nextpage" href="../aceintro/">Introduction to ACE Models »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.7.0 on <span class="colophon-date" title="Wednesday 11 September 2024 18:50">Wednesday 11 September 2024</span>. Using Julia version 1.10.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>