update(gh-pages/v1.4)

Update.
Now the main part of the documentation finishes.

v1.4/index.html

@@ -9,4 +9,4 @@
 # In pkg mode of REPL:
 # (@v1.8) pkg&gt; add [email protected]</code></pre><p>It is shown that <em>[email protected]</em> and <em>[email protected]</em> runs well on Windows 10 (10.0.19044) and WSL Ubuntu (22.04.1 LTS).</p></div></div><h3 id="Configuring-Python-and-PySCF"><a class="docs-heading-anchor" href="#Configuring-Python-and-PySCF">Configuring Python and PySCF</a><a id="Configuring-Python-and-PySCF-1"></a><a class="docs-heading-anchor-permalink" href="#Configuring-Python-and-PySCF" title="Permalink"></a></h3><p>Currently the <a href="theory1_initial_conditions/#MOADK">MO-ADK</a> and <a href="theory1_initial_conditions/#WFAT">WFAT</a> features related to molecules rely on the <a href="https://github.com/pyscf/pyscf">PySCF</a> python package. <em>SemiclassicalSFI.jl</em> calls the PySCF using the <a href="https://github.com/JuliaPy/PyCall.jl">PyCall.jl</a> package. There are two ways to set up the Python environment used by PyCall, here we suggest using your local Python environment for convenience.</p><p>To correctly set up the configuration of PyCall, first, set the <code>PYTHON</code> environment variable to your Python executable, and build the PyCall package:</p><pre><code class="language-julia hljs">ENV[&quot;PYTHON&quot;] = &quot;path/to/python_exec&quot;
 using Pkg
-Pkg.build(&quot;PyCall&quot;)</code></pre><p>And don&#39;t forget to install PySCF in your Python via pip:</p><pre><code class="nohighlight hljs">$ pip3 install pyscf</code></pre><div class="admonition is-info"><header class="admonition-header">Note</header><div class="admonition-body"><p>Since the PySCF does not support the Windows, the molecular calculation must be performed on a Linux or macOS platform. However, for Windows users, they may install the <a href="https://learn.microsoft.com/en-us/windows/wsl/install">WSL</a> (Windows Subsystem for Linux), which supports the PySCF.</p></div></div><h2 id="Contributors"><a class="docs-heading-anchor" href="#Contributors">Contributors</a><a id="Contributors-1"></a><a class="docs-heading-anchor-permalink" href="#Contributors" title="Permalink"></a></h2><ul><li><a href="https://github.com/TheStarAlight">Mingyu Zhu</a> @ ECNU</li><li><a href="https://faculty.ecnu.edu.cn/_s29/nhc_en/main.psp">Hongcheng Ni</a> @ ECNU</li></ul><h2 id="License"><a class="docs-heading-anchor" href="#License">License</a><a id="License-1"></a><a class="docs-heading-anchor-permalink" href="#License" title="Permalink"></a></h2><p>This package is licensed under the Apache 2.0 license, and is copyrighted by Mingyu Zhu, Hongcheng Ni and the other contributors.</p><section class="footnotes is-size-7"><ul><li class="footnote" id="footnote-Corkum_1989"><a class="tag is-link" href="#citeref-Corkum_1989">Corkum_1989</a>P. B. Corkum <em>et al.</em>, Above-Threshold Ionization in the Long-Wavelength Limit. <em>Phys. Rev. Lett.</em> <strong>62</strong>(11), 1259–1262 (1989). DOI: <a href="https://dx.doi.org/10.1103/PhysRevLett.62.1259">10.1103/PhysRevLett.62.1259</a></li><li class="footnote" id="footnote-Hu_1997"><a class="tag is-link" href="#citeref-Hu_1997">Hu_1997</a>B. Hu <em>et al.</em>, Plateau in Above-Threshold-Ionization Spectra and Chaotic Behavior in Rescattering Processes. <em>Phys. Lett. A</em> <strong>236</strong>, 533–542 (1997). DOI: <a href="https://dx.doi.org/10.1016/S0375-9601(97)00811-6">10.1016/S0375-9601(97)00811-6</a></li></ul></section></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="theory1_initial_conditions/">Initial Conditions »</a><div class="flexbox-break"></div><p class="footer-message">· <em>SemiclassicalSFI.jl</em> Documentation · by <em>Mingyu Zhu</em> and other contributors</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Sunday 23 July 2023 10:59">Sunday 23 July 2023</span>. Using Julia version 1.8.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+Pkg.build(&quot;PyCall&quot;)</code></pre><p>And don&#39;t forget to install PySCF in your Python via pip:</p><pre><code class="nohighlight hljs">$ pip3 install pyscf</code></pre><div class="admonition is-info"><header class="admonition-header">Note</header><div class="admonition-body"><p>Since the PySCF does not support the Windows, the molecular calculation must be performed on a Linux or macOS platform. However, for Windows users, they may install the <a href="https://learn.microsoft.com/en-us/windows/wsl/install">WSL</a> (Windows Subsystem for Linux), which supports the PySCF.</p></div></div><h2 id="Contributors"><a class="docs-heading-anchor" href="#Contributors">Contributors</a><a id="Contributors-1"></a><a class="docs-heading-anchor-permalink" href="#Contributors" title="Permalink"></a></h2><ul><li><a href="https://github.com/TheStarAlight">Mingyu Zhu</a> @ ECNU</li><li><a href="https://faculty.ecnu.edu.cn/_s29/nhc_en/main.psp">Hongcheng Ni</a> @ ECNU</li></ul><h2 id="License"><a class="docs-heading-anchor" href="#License">License</a><a id="License-1"></a><a class="docs-heading-anchor-permalink" href="#License" title="Permalink"></a></h2><p>This package is licensed under the Apache 2.0 license, and is copyrighted by Mingyu Zhu, Hongcheng Ni and the other contributors.</p><section class="footnotes is-size-7"><ul><li class="footnote" id="footnote-Corkum_1989"><a class="tag is-link" href="#citeref-Corkum_1989">Corkum_1989</a>P. B. Corkum <em>et al.</em>, Above-Threshold Ionization in the Long-Wavelength Limit. <em>Phys. Rev. Lett.</em> <strong>62</strong>(11), 1259–1262 (1989). DOI: <a href="https://dx.doi.org/10.1103/PhysRevLett.62.1259">10.1103/PhysRevLett.62.1259</a></li><li class="footnote" id="footnote-Hu_1997"><a class="tag is-link" href="#citeref-Hu_1997">Hu_1997</a>B. Hu <em>et al.</em>, Plateau in Above-Threshold-Ionization Spectra and Chaotic Behavior in Rescattering Processes. <em>Phys. Lett. A</em> <strong>236</strong>, 533–542 (1997). DOI: <a href="https://dx.doi.org/10.1016/S0375-9601(97)00811-6">10.1016/S0375-9601(97)00811-6</a></li></ul></section></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="theory1_initial_conditions/">Initial Conditions »</a><div class="flexbox-break"></div><p class="footer-message">· <em>SemiclassicalSFI.jl</em> Documentation · by <em>Mingyu Zhu</em> and other contributors</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Sunday 23 July 2023 14:09">Sunday 23 July 2023</span>. Using Julia version 1.8.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

v1.4/manual1_targets/index.html

@@ -43,4 +43,4 @@
     grid_ϕNum::Int  = 60,
     l_max::Int      = 6,
     m_max::Int      = 3,
-    kwargs...)</code></pre><p>Calculates the MOADK coefficients of the given molecule.</p><p><strong>Parameters</strong></p><ul><li><code>mc</code>              : The molecular calculator.</li><li><code>orbitIdx_relHOMO</code>: Index of selected orbit relative to the HOMO (e.g., 0 indicates HOMO and -1 indicates HOMO-1) (default 0).</li><li><code>grid_rNum</code>       : The number of radial grid (default 200).</li><li><code>grid_rReg</code>       : The region of radial distance to fit the wavefunction to obtain the coefficients (default (3,8)).</li><li><code>grid_θNum</code>       : The number of angular grid in the <span>$θ$</span> direction (default 60).</li><li><code>grid_ϕNum</code>       : The number of angular grid in the <span>$ϕ$</span> direction (default 60).</li><li><code>l_max</code>           : The maximum number of <span>$l$</span> calculated (default 6).</li><li><code>m_max</code>           : The maximum number of <span>$m$</span> calculated (default 3).</li></ul></div></section></article><h3 id="Molecule&#39;s-Orientation"><a class="docs-heading-anchor" href="#Molecule&#39;s-Orientation">Molecule&#39;s Orientation</a><a id="Molecule&#39;s-Orientation-1"></a><a class="docs-heading-anchor-permalink" href="#Molecule&#39;s-Orientation" title="Permalink"></a></h3><p>The molecule&#39;s orientation is described by a set of Euler angles (<span>$z-y&#39;-z&#39;&#39;$</span> convention), which defines a rotational transformation from the molecular frame (MF) to the lab frame (LF). This property of <code>Molecule</code> is NOT included in the saved file and thus needs to be specified each time upon initialization of the <code>Molecule</code> object from external files.</p><div class="admonition is-info"><header class="admonition-header">Note</header><div class="admonition-body"><p>Here the three Euler angles <code>(α,β,γ)</code> that describe the <code>Molecule</code>&#39;s orientation are completely different from that of the Euler angles <code>(β&#39;,γ&#39;)</code> in the <a href="../theory1_initial_conditions/#WFAT">WFAT</a> and <a href="../theory1_initial_conditions/#MOADK">MO-ADK</a> theory. These theories&#39; &quot;lab frame&quot; is chosen for convenience of theoretical formulation, where the electric field is assumed to be static, pointing towards the <span>$+z$</span> direction, and has no relation with the lab frame mentioned above.</p></div></div><p>The orientation of the molecule can be obtained and set via the <a href="#SemiclassicalSFI.Targets.MolRotation"><code>MolRotation</code></a> and <a href="#SemiclassicalSFI.Targets.SetMolRotation"><code>SetMolRotation</code></a> methods.</p><article class="docstring"><header><a class="docstring-binding" id="SemiclassicalSFI.Targets.MolRotation" href="#SemiclassicalSFI.Targets.MolRotation"><code>SemiclassicalSFI.Targets.MolRotation</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">MolRotation(mol::Molecule)</code></pre><p>Gets the Euler angles (ZYZ convention) specifying the molecule&#39;s orientation in format (α,β,γ).</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="SemiclassicalSFI.Targets.SetMolRotation" href="#SemiclassicalSFI.Targets.SetMolRotation"><code>SemiclassicalSFI.Targets.SetMolRotation</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">SetMolRotation(mol::Molecule, α,β,γ)</code></pre><p>Sets the Euler angles (ZYZ convention) specifying the molecule&#39;s orientation in format (α,β,γ).</p></div></section><section><div><pre><code class="nohighlight hljs">SetMolRotation(mol::Molecule, (α,β,γ))</code></pre><p>Sets the Euler angles (ZYZ convention) specifying the molecule&#39;s orientation in format (α,β,γ).</p></div></section></article><section class="footnotes is-size-7"><ul><li class="footnote" id="footnote-Tong_2005"><a class="tag is-link" href="#citeref-Tong_2005">Tong_2005</a>X. M. Tong <em>et al.</em>, Empirical Formula for Static Field Ionization Rates of Atoms and Molecules by Lasers in the Barrier-Suppression Regime. <em>J. Phys. B: At. Mol. Opt. Phys.</em> <strong>38</strong>, 2593–2600. DOI: <a href="https://dx.doi.org/10.1088/0953-4075/38/15/001">10.1088/0953-4075/38/15/001</a></li><li class="footnote" id="footnote-note"><a class="tag is-link" href="#citeref-note">note</a>The symbols of the parameters are different from that in the original article. <span>$a_1, b_1, a_2, b_2, a_3, b_3$</span> correspond to <span>$a_1, a_2, a_3, a_4, a_5, a_6$</span> in the original article respectively.</li></ul></section></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../theory2_trajectory_simulation_phase_methods/">« Trajectory Simulation and Phase Methods</a><a class="docs-footer-nextpage" href="../manual2_lasers/">Lasers »</a><div class="flexbox-break"></div><p class="footer-message">· <em>SemiclassicalSFI.jl</em> Documentation · by <em>Mingyu Zhu</em> and other contributors</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Sunday 23 July 2023 10:59">Sunday 23 July 2023</span>. Using Julia version 1.8.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+    kwargs...)</code></pre><p>Calculates the MOADK coefficients of the given molecule.</p><p><strong>Parameters</strong></p><ul><li><code>mc</code>              : The molecular calculator.</li><li><code>orbitIdx_relHOMO</code>: Index of selected orbit relative to the HOMO (e.g., 0 indicates HOMO and -1 indicates HOMO-1) (default 0).</li><li><code>grid_rNum</code>       : The number of radial grid (default 200).</li><li><code>grid_rReg</code>       : The region of radial distance to fit the wavefunction to obtain the coefficients (default (3,8)).</li><li><code>grid_θNum</code>       : The number of angular grid in the <span>$θ$</span> direction (default 60).</li><li><code>grid_ϕNum</code>       : The number of angular grid in the <span>$ϕ$</span> direction (default 60).</li><li><code>l_max</code>           : The maximum number of <span>$l$</span> calculated (default 6).</li><li><code>m_max</code>           : The maximum number of <span>$m$</span> calculated (default 3).</li></ul></div></section></article><h3 id="Molecule&#39;s-Orientation"><a class="docs-heading-anchor" href="#Molecule&#39;s-Orientation">Molecule&#39;s Orientation</a><a id="Molecule&#39;s-Orientation-1"></a><a class="docs-heading-anchor-permalink" href="#Molecule&#39;s-Orientation" title="Permalink"></a></h3><p>The molecule&#39;s orientation is described by a set of Euler angles (<span>$z-y&#39;-z&#39;&#39;$</span> convention), which defines a rotational transformation from the molecular frame (MF) to the lab frame (LF). This property of <code>Molecule</code> is NOT included in the saved file and thus needs to be specified each time upon initialization of the <code>Molecule</code> object from external files.</p><div class="admonition is-info"><header class="admonition-header">Note</header><div class="admonition-body"><p>Here the three Euler angles <code>(α,β,γ)</code> that describe the <code>Molecule</code>&#39;s orientation are completely different from that of the Euler angles <code>(β&#39;,γ&#39;)</code> in the <a href="../theory1_initial_conditions/#WFAT">WFAT</a> and <a href="../theory1_initial_conditions/#MOADK">MO-ADK</a> theory. These theories&#39; &quot;lab frame&quot; is chosen for convenience of theoretical formulation, where the electric field is assumed to be static, pointing towards the <span>$+z$</span> direction, and has no relation with the lab frame mentioned above.</p></div></div><p>The orientation of the molecule can be obtained and set via the <a href="#SemiclassicalSFI.Targets.MolRotation"><code>MolRotation</code></a> and <a href="#SemiclassicalSFI.Targets.SetMolRotation"><code>SetMolRotation</code></a> methods.</p><article class="docstring"><header><a class="docstring-binding" id="SemiclassicalSFI.Targets.MolRotation" href="#SemiclassicalSFI.Targets.MolRotation"><code>SemiclassicalSFI.Targets.MolRotation</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">MolRotation(mol::Molecule)</code></pre><p>Gets the Euler angles (ZYZ convention) specifying the molecule&#39;s orientation in format (α,β,γ).</p></div></section></article><article class="docstring"><header><a class="docstring-binding" id="SemiclassicalSFI.Targets.SetMolRotation" href="#SemiclassicalSFI.Targets.SetMolRotation"><code>SemiclassicalSFI.Targets.SetMolRotation</code></a> — <span class="docstring-category">Function</span></header><section><div><pre><code class="language-julia hljs">SetMolRotation(mol::Molecule, α,β,γ)</code></pre><p>Sets the Euler angles (ZYZ convention) specifying the molecule&#39;s orientation in format (α,β,γ).</p></div></section><section><div><pre><code class="nohighlight hljs">SetMolRotation(mol::Molecule, (α,β,γ))</code></pre><p>Sets the Euler angles (ZYZ convention) specifying the molecule&#39;s orientation in format (α,β,γ).</p></div></section></article><section class="footnotes is-size-7"><ul><li class="footnote" id="footnote-Tong_2005"><a class="tag is-link" href="#citeref-Tong_2005">Tong_2005</a>X. M. Tong <em>et al.</em>, Empirical Formula for Static Field Ionization Rates of Atoms and Molecules by Lasers in the Barrier-Suppression Regime. <em>J. Phys. B: At. Mol. Opt. Phys.</em> <strong>38</strong>, 2593–2600. DOI: <a href="https://dx.doi.org/10.1088/0953-4075/38/15/001">10.1088/0953-4075/38/15/001</a></li><li class="footnote" id="footnote-note"><a class="tag is-link" href="#citeref-note">note</a>The symbols of the parameters are different from that in the original article. <span>$a_1, b_1, a_2, b_2, a_3, b_3$</span> correspond to <span>$a_1, a_2, a_3, a_4, a_5, a_6$</span> in the original article respectively.</li></ul></section></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../theory2_trajectory_simulation_phase_methods/">« Trajectory Simulation and Phase Methods</a><a class="docs-footer-nextpage" href="../manual2_lasers/">Lasers »</a><div class="flexbox-break"></div><p class="footer-message">· <em>SemiclassicalSFI.jl</em> Documentation · by <em>Mingyu Zhu</em> and other contributors</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.25 on <span class="colophon-date" title="Sunday 23 July 2023 14:09">Sunday 23 July 2023</span>. Using Julia version 1.8.5.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>