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Better doc
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@ -17,10 +17,10 @@
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Data structure for Gaussian Atomic Orbitals:
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$$
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\chi(r) = P(X_A,Y_A,Z_A) \sum_k a_k \exp\left( -\alpha_k (\mathbf{r-R_A})^2 \right)
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\chi_i(\mathbf{r}) = P_i(\mathbf{r}) \sum_k c_k \exp\left( -\alpha_k (\mathbf{r-R_A})^2 \right)
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$$
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where the polynomial $P$ and the Gaussian part are both centered on
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where the polynomial $P_Ai and the Gaussian part are both centered on
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nucleus $A$.
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** Type
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96
docs/ao.html
96
docs/ao.html
@ -3,7 +3,7 @@
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
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<head>
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<!-- 2021-01-04 Mon 23:37 -->
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<!-- 2021-01-04 Mon 23:51 -->
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
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<meta name="viewport" content="width=device-width, initial-scale=1" />
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<title>Atomic Orbitals</title>
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@ -251,36 +251,36 @@
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<h2>Table of Contents</h2>
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<div id="text-table-of-contents">
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<ul>
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<li><a href="#org85ad534">1. Gaussian basis</a>
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<li><a href="#orgdad2461">1. Gaussian basis</a>
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<ul>
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<li><a href="#orgd5272b4">1.1. Type</a></li>
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<li><a href="#orgaf2c5e0">1.2. Access</a></li>
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<li><a href="#org2ef05ff">1.3. Computation</a></li>
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<li><a href="#orgc96dbf4">1.4. Creation</a></li>
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<li><a href="#org2ad4cb4">1.5. Printers</a></li>
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<li><a href="#org74f68e8">1.1. Type</a></li>
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<li><a href="#orgfdc3c55">1.2. Access</a></li>
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<li><a href="#org1c0d454">1.3. Computation</a></li>
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<li><a href="#org79e7f88">1.4. Creation</a></li>
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<li><a href="#org94dcdb9">1.5. Printers</a></li>
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</ul>
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</li>
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<li><a href="#org0b46c53">2. Basis</a>
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<li><a href="#orga689f4e">2. Basis</a>
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<ul>
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<li><a href="#org92f0c67">2.1. Dimensions   <span class="tag"><span class="noexports">noexports</span></span></a></li>
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<li><a href="#org30491e1">2.2. Polymorphic types</a></li>
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<li><a href="#org7349692">2.3. Types</a></li>
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<li><a href="#org7ec971a">2.4. Conversions</a></li>
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<li><a href="#orgae6a1f6">2.5. Access</a></li>
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<li><a href="#orgaa19d01">2.6. Printers</a></li>
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<li><a href="#orgfd1c95a">2.1. Dimensions   <span class="tag"><span class="noexports">noexports</span></span></a></li>
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<li><a href="#org3d84ea0">2.2. Polymorphic types</a></li>
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<li><a href="#org709c411">2.3. Types</a></li>
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<li><a href="#org963f093">2.4. Conversions</a></li>
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<li><a href="#org72dcc0e">2.5. Access</a></li>
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<li><a href="#org4161331">2.6. Printers</a></li>
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</ul>
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</li>
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</ul>
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</div>
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</div>
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<div class="org-src-container">
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<pre class="src src-ocaml" id="org9946305"><span class="org-string">"Atomic basis set"</span>
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<pre class="src src-ocaml" id="org4eaf45c"><span class="org-string">"Atomic basis set"</span>
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</pre>
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</div>
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<div id="outline-container-org85ad534" class="outline-2">
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<h2 id="org85ad534"><span class="section-number-2">1</span> Gaussian basis</h2>
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<div id="outline-container-orgdad2461" class="outline-2">
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<h2 id="orgdad2461"><span class="section-number-2">1</span> Gaussian basis</h2>
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<div class="outline-text-2" id="text-1">
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<p>
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Data structure for Gaussian Atomic Orbitals:
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@ -288,21 +288,21 @@ Data structure for Gaussian Atomic Orbitals:
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<p>
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\[
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\chi(r) = P(X_A,Y_A,Z_A) \sum_k a_k \exp\left( -\alpha_k (\mathbf{r-R_A})^2 \right)
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\chi_i(\mathbf{r}) = P_i(\mathbf{r}) \sum_k c_k \exp\left( -\alpha_k (\mathbf{r-R_A})^2 \right)
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\]
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</p>
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<p>
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where the polynomial \(P\) and the Gaussian part are both centered on
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where the polynomial $P<sub>Ai</sub> and the Gaussian part are both centered on
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nucleus \(A\).
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</p>
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</div>
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<div id="outline-container-orgd5272b4" class="outline-3">
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<h3 id="orgd5272b4"><span class="section-number-3">1.1</span> Type</h3>
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<div id="outline-container-org74f68e8" class="outline-3">
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<h3 id="org74f68e8"><span class="section-number-3">1.1</span> Type</h3>
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<div class="outline-text-3" id="text-1-1">
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<div class="org-src-container">
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<pre class="src src-ocaml" id="orgfc52bc7"><span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Common</span>
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<pre class="src src-ocaml" id="orga6cc859"><span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Common</span>
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<span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Particles</span>
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<span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Linear_algebra</span>
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<span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Gaussian_integrals</span>
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@ -314,8 +314,8 @@ nucleus \(A\).
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</div>
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</div>
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<div id="outline-container-orgaf2c5e0" class="outline-3">
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<h3 id="orgaf2c5e0"><span class="section-number-3">1.2</span> Access</h3>
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<div id="outline-container-orgfdc3c55" class="outline-3">
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<h3 id="orgfdc3c55"><span class="section-number-3">1.2</span> Access</h3>
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<div class="outline-text-3" id="text-1-2">
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<div class="org-src-container">
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<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">basis</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> <span class="org-tuareg-font-lock-module">Gaussian.Basis.</span>t
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@ -406,8 +406,8 @@ nucleus \(A\).
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</div>
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</div>
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<div id="outline-container-org2ef05ff" class="outline-3">
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<h3 id="org2ef05ff"><span class="section-number-3">1.3</span> Computation</h3>
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<div id="outline-container-org1c0d454" class="outline-3">
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<h3 id="org1c0d454"><span class="section-number-3">1.3</span> Computation</h3>
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<div class="outline-text-3" id="text-1-3">
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<div class="org-src-container">
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<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">values</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> <span class="org-tuareg-font-lock-module">Coordinate.</span>t <span class="org-tuareg-font-lock-operator">-></span> <span class="org-tuareg-font-lock-module">Gaussian.Basis.</span>t <span class="org-tuareg-font-lock-module">Vector.</span>t
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@ -432,8 +432,8 @@ nucleus \(A\).
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</div>
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</div>
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<div id="outline-container-orgc96dbf4" class="outline-3">
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<h3 id="orgc96dbf4"><span class="section-number-3">1.4</span> Creation</h3>
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<div id="outline-container-org79e7f88" class="outline-3">
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<h3 id="org79e7f88"><span class="section-number-3">1.4</span> Creation</h3>
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<div class="outline-text-3" id="text-1-4">
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<div class="org-src-container">
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<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">make</span> <span class="org-tuareg-font-lock-operator">:</span> <span class="org-tuareg-font-lock-label">basis</span><span class="org-tuareg-font-lock-operator">:</span><span class="org-tuareg-font-lock-module">Gaussian.Basis.</span>t <span class="org-tuareg-font-lock-operator">-></span>
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@ -456,15 +456,15 @@ Defaults:
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<li><code>cartesian</code> : <code>false</code></li>
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</ul>
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<pre class="example" id="org2235be7">
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<pre class="example" id="org2cdf9ac">
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let b = Ao.Basis_gaussian.make ~basis nuclei ;;
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val b : Ao.Basis_gaussian.t = Gaussian Basis, spherical, 15 AOs
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</pre>
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</div>
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</div>
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<div id="outline-container-org2ad4cb4" class="outline-3">
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<h3 id="org2ad4cb4"><span class="section-number-3">1.5</span> Printers</h3>
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<div id="outline-container-org94dcdb9" class="outline-3">
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<h3 id="org94dcdb9"><span class="section-number-3">1.5</span> Printers</h3>
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<div class="outline-text-3" id="text-1-5">
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<div class="org-src-container">
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<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">pp</span> <span class="org-tuareg-font-lock-operator">:</span> <span class="org-tuareg-font-lock-module">Format.</span>formatter <span class="org-tuareg-font-lock-operator">-></span> t <span class="org-tuareg-font-lock-operator">-></span> unit
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@ -474,23 +474,23 @@ val b : Ao.Basis_gaussian.t = Gaussian Basis, spherical, 15 AOs
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</div>
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</div>
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<div id="outline-container-org0b46c53" class="outline-2">
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<h2 id="org0b46c53"><span class="section-number-2">2</span> Basis</h2>
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<div id="outline-container-orga689f4e" class="outline-2">
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<h2 id="orga689f4e"><span class="section-number-2">2</span> Basis</h2>
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<div class="outline-text-2" id="text-2">
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<p>
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Data structure for Atomic Orbitals.
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</p>
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</div>
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<div id="outline-container-org92f0c67" class="outline-3">
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<h3 id="org92f0c67"><span class="section-number-3">2.1</span> Dimensions   <span class="tag"><span class="noexports">noexports</span></span></h3>
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<div id="outline-container-orgfd1c95a" class="outline-3">
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||||
<h3 id="orgfd1c95a"><span class="section-number-3">2.1</span> Dimensions   <span class="tag"><span class="noexports">noexports</span></span></h3>
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</div>
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<div id="outline-container-org30491e1" class="outline-3">
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<h3 id="org30491e1"><span class="section-number-3">2.2</span> Polymorphic types</h3>
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<div id="outline-container-org3d84ea0" class="outline-3">
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<h3 id="org3d84ea0"><span class="section-number-3">2.2</span> Polymorphic types</h3>
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<div class="outline-text-3" id="text-2-2">
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<div class="org-src-container">
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<pre class="src src-ocaml" id="org2d5449d"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span> <span class="org-tuareg-font-lock-operator">=</span>
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<pre class="src src-ocaml" id="org8858f18"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span> <span class="org-tuareg-font-lock-operator">=</span>
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<span class="org-tuareg-font-lock-operator">|</span> <span class="org-tuareg-font-lock-constructor">Unknown</span>
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<span class="org-tuareg-font-lock-operator">|</span> <span class="org-tuareg-font-lock-constructor">Gaussian</span> <span class="org-keyword">of</span> <span class="org-tuareg-font-lock-module">Basis_gaussian.</span>t
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</pre>
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@ -498,8 +498,8 @@ Data structure for Atomic Orbitals.
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</div>
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</div>
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<div id="outline-container-org7349692" class="outline-3">
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<h3 id="org7349692"><span class="section-number-3">2.3</span> Types</h3>
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<div id="outline-container-org709c411" class="outline-3">
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<h3 id="org709c411"><span class="section-number-3">2.3</span> Types</h3>
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<div class="outline-text-3" id="text-2-3">
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<div class="org-src-container">
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<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span>
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@ -514,8 +514,8 @@ Data structure for Atomic Orbitals.
|
||||
</div>
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</div>
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<div id="outline-container-org7ec971a" class="outline-3">
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<h3 id="org7ec971a"><span class="section-number-3">2.4</span> Conversions</h3>
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<div id="outline-container-org963f093" class="outline-3">
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<h3 id="org963f093"><span class="section-number-3">2.4</span> Conversions</h3>
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<div class="outline-text-3" id="text-2-4">
|
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<div class="org-src-container">
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<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">of_nuclei_and_basis_filename</span> <span class="org-tuareg-font-lock-operator">:</span>
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@ -549,15 +549,15 @@ Defaults:
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<li><code>cartesian</code> : <code>false</code></li>
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</ul>
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<pre class="example" id="orgaf90516">
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<pre class="example" id="org8d860d9">
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let b = Ao.Basis.of_nuclei_and_basis_filename ~nuclei filename;;
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val b : Ao.Basis.t = Gaussian Basis, spherical, 15 AOs
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</pre>
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||||
</div>
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</div>
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||||
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<div id="outline-container-orgae6a1f6" class="outline-3">
|
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<h3 id="orgae6a1f6"><span class="section-number-3">2.5</span> Access</h3>
|
||||
<div id="outline-container-org72dcc0e" class="outline-3">
|
||||
<h3 id="org72dcc0e"><span class="section-number-3">2.5</span> Access</h3>
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<div class="outline-text-3" id="text-2-5">
|
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<div class="org-src-container">
|
||||
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">size</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> int
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||||
@ -655,8 +655,8 @@ val b : Ao.Basis.t = Gaussian Basis, spherical, 15 AOs
|
||||
</div>
|
||||
|
||||
|
||||
<div id="outline-container-orgaa19d01" class="outline-3">
|
||||
<h3 id="orgaa19d01"><span class="section-number-3">2.6</span> Printers</h3>
|
||||
<div id="outline-container-org4161331" class="outline-3">
|
||||
<h3 id="org4161331"><span class="section-number-3">2.6</span> Printers</h3>
|
||||
<div class="outline-text-3" id="text-2-6">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">pp</span> <span class="org-tuareg-font-lock-operator">:</span> <span class="org-tuareg-font-lock-module">Format.</span>formatter <span class="org-tuareg-font-lock-operator">-></span> t <span class="org-tuareg-font-lock-operator">-></span> unit
|
||||
@ -668,7 +668,7 @@ val b : Ao.Basis.t = Gaussian Basis, spherical, 15 AOs
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: Anthony Scemama</p>
|
||||
<p class="date">Created: 2021-01-04 Mon 23:37</p>
|
||||
<p class="date">Created: 2021-01-04 Mon 23:51</p>
|
||||
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
@ -3,7 +3,7 @@
|
||||
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
|
||||
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
|
||||
<head>
|
||||
<!-- 2021-01-04 Mon 23:32 -->
|
||||
<!-- 2021-01-04 Mon 23:47 -->
|
||||
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1" />
|
||||
<title>QCaml documentation</title>
|
||||
@ -229,21 +229,21 @@
|
||||
<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
|
||||
<li><a href="#org5867ef0">1. Documentation of Modules</a></li>
|
||||
<li><a href="#org8320997">1. Documentation of Modules</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="orgd9ea58a" class="figure">
|
||||
<p><img src="./chamo_bg.png" alt="chamo_bg.png" />
|
||||
</p>
|
||||
</div>
|
||||
|
||||
<p>
|
||||
QCaml is an OCaml library for writing quantum chemistry codes.
|
||||
It is written using literate programming with org-mode.
|
||||
</p>
|
||||
|
||||
|
||||
<div id="org0374b1d" class="figure">
|
||||
<p><img src="./chamo_bg.png" alt="chamo_bg.png" />
|
||||
</p>
|
||||
</div>
|
||||
|
||||
<p>
|
||||
To use it interactively in the top level or in a Jupyter or org-mode
|
||||
notebook, use
|
||||
@ -259,30 +259,29 @@ This loads all the sub-libraries provided with QCaml, and installs
|
||||
the pretty printers.
|
||||
</p>
|
||||
|
||||
<div id="outline-container-org5867ef0" class="outline-2">
|
||||
<h2 id="org5867ef0"><span class="section-number-2">1</span> Documentation of Modules</h2>
|
||||
<div id="outline-container-org8320997" class="outline-2">
|
||||
<h2 id="org8320997"><span class="section-number-2">1</span> Documentation of Modules</h2>
|
||||
<div class="outline-text-2" id="text-1">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-org">- <span class="org-org-link"><a href="./ao.html">Ao</a></span>
|
||||
- <span class="org-org-link"><a href="./common.html">Common</a></span>
|
||||
- <span class="org-org-link"><a href="./gaussian_integrals.html">Gaussian_integrals</a></span>
|
||||
- <span class="org-org-link"><a href="./gaussian.html">Gaussian</a></span>
|
||||
- <span class="org-org-link"><a href="./linear_algebra.html">Linear_algebra</a></span>
|
||||
- <span class="org-org-link"><a href="./mo.html">Mo</a></span>
|
||||
- <span class="org-org-link"><a href="./operators.html">Operators</a></span>
|
||||
- <span class="org-org-link"><a href="./particles.html">Particles</a></span>
|
||||
- <span class="org-org-link"><a href="./perturbation.html">Perturbation</a></span>
|
||||
- <span class="org-org-link"><a href="./qcaml.html">Qcaml</a></span>
|
||||
- <span class="org-org-link"><a href="./simulation.html">Simulation</a></span>
|
||||
- <span class="org-org-link"><a href="./top.html">Top</a></span>
|
||||
</pre>
|
||||
</div>
|
||||
<ul class="org-ul">
|
||||
<li><a href="./ao.html">Ao</a></li>
|
||||
<li><a href="./common.html">Common</a></li>
|
||||
<li><a href="./gaussian_integrals.html">Gaussian integrals</a></li>
|
||||
<li><a href="./gaussian.html">Gaussian</a></li>
|
||||
<li><a href="./linear_algebra.html">Linear algebra</a></li>
|
||||
<li><a href="./mo.html">Mo</a></li>
|
||||
<li><a href="./operators.html">Operators</a></li>
|
||||
<li><a href="./particles.html">Particles</a></li>
|
||||
<li><a href="./perturbation.html">Perturbation</a></li>
|
||||
<li><a href="./qcaml.html">Qcaml</a></li>
|
||||
<li><a href="./simulation.html">Simulation</a></li>
|
||||
<li><a href="./top.html">Top</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: Anthony Scemama</p>
|
||||
<p class="date">Created: 2021-01-04 Mon 23:32</p>
|
||||
<p class="date">Created: 2021-01-04 Mon 23:47</p>
|
||||
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
@ -1,12 +1,11 @@
|
||||
#+TITLE: QCaml documentation
|
||||
#+SETUPFILE: ../docs/org-html-themes/org/theme-readtheorg.setup
|
||||
|
||||
|
||||
[[./chamo_bg.png]]
|
||||
|
||||
QCaml is an OCaml library for writing quantum chemistry codes.
|
||||
It is written using literate programming with org-mode.
|
||||
|
||||
[[./chamo_bg.png]]
|
||||
|
||||
To use it interactively in the top level or in a Jupyter or org-mode
|
||||
notebook, use
|
||||
|
||||
@ -19,13 +18,50 @@
|
||||
|
||||
* Documentation of Modules
|
||||
|
||||
#+NAME: list
|
||||
#+begin_src sh :exports results :results org
|
||||
#+NAME: modules
|
||||
#+begin_src sh :exports none
|
||||
ls ../*/README.org \
|
||||
| cut -d '/' -f 2 \
|
||||
| sed 's/[^.]*/- \[\[.\/&\.html\]\[\u&\]\]/g'
|
||||
| cut -d '/' -f 2
|
||||
#+end_src
|
||||
|
||||
#+RESULTS: modules
|
||||
| ao |
|
||||
| common |
|
||||
| gaussian_integrals |
|
||||
| gaussian |
|
||||
| linear_algebra |
|
||||
| mo |
|
||||
| operators |
|
||||
| particles |
|
||||
| perturbation |
|
||||
| qcaml |
|
||||
| simulation |
|
||||
| top |
|
||||
|
||||
#+NAME: list
|
||||
#+begin_src python :var modules=modules :exports results :results output drawer
|
||||
for m in modules:
|
||||
m = m[0]
|
||||
m2 = m.replace("_"," ").capitalize()
|
||||
print(f"- [[./{m}.html][{m2}]]")
|
||||
#+end_src
|
||||
|
||||
#+RESULTS: list
|
||||
:results:
|
||||
- [[./ao.html][Ao]]
|
||||
- [[./common.html][Common]]
|
||||
- [[./gaussian_integrals.html][Gaussian integrals]]
|
||||
- [[./gaussian.html][Gaussian]]
|
||||
- [[./linear_algebra.html][Linear algebra]]
|
||||
- [[./mo.html][Mo]]
|
||||
- [[./operators.html][Operators]]
|
||||
- [[./particles.html][Particles]]
|
||||
- [[./perturbation.html][Perturbation]]
|
||||
- [[./qcaml.html][Qcaml]]
|
||||
- [[./simulation.html][Simulation]]
|
||||
- [[./top.html][Top]]
|
||||
:end:
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
@ -3,7 +3,7 @@
|
||||
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
|
||||
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
|
||||
<head>
|
||||
<!-- 2021-01-04 Mon 23:37 -->
|
||||
<!-- 2021-01-04 Mon 23:51 -->
|
||||
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1" />
|
||||
<title>Top-level</title>
|
||||
@ -226,13 +226,13 @@
|
||||
<div id="content">
|
||||
<h1 class="title">Top-level</h1>
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-ocaml" id="org358e627"><span class="org-string">"Installs pretty printers for top-level."</span>
|
||||
<pre class="src src-ocaml" id="org6a155c1"><span class="org-string">"Installs pretty printers for top-level."</span>
|
||||
</pre>
|
||||
</div>
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: Anthony Scemama</p>
|
||||
<p class="date">Created: 2021-01-04 Mon 23:37</p>
|
||||
<p class="date">Created: 2021-01-04 Mon 23:51</p>
|
||||
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
Loading…
Reference in New Issue
Block a user