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This commit is contained in:
Anthony Scemama 2021-10-19 16:57:22 +02:00
parent 83f562aadf
commit 98ca250ed3
18 changed files with 494 additions and 494 deletions
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docs/common.html
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docs/gaussian.html
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@ -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>
<!-- 2021-01-27 Wed 23:44 -->
<!-- 2021-10-19 Tue 16:20 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Gaussian</title>
@ -272,41 +272,41 @@ org_html_manager.setup(); // activate after the parameters are set
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgf3ada33">1. Summmary</a></li>
<li><a href="#org7457529">2. Atomic shell</a>
<li><a href="#org458f6db">1. Summary</a></li>
<li><a href="#org000b493">2. Atomic shell</a>
<ul>
<li><a href="#org0e4fe4d">2.1. Type</a></li>
<li><a href="#orgde1bce4">2.2. Access</a></li>
<li><a href="#org24b2b8e">2.3. Creation</a></li>
<li><a href="#orge729f26">2.4. Printers</a></li>
<li><a href="#orgd5a7f6d">2.1. Type</a></li>
<li><a href="#org3d580ec">2.2. Access</a></li>
<li><a href="#org2a3c76d">2.3. Creation</a></li>
<li><a href="#orge3b7bbf">2.4. Printers</a></li>
</ul>
</li>
<li><a href="#org8871eba">3. Atomic shell pair couple</a>
<li><a href="#org403784b">3. Atomic shell pair couple</a>
<ul>
<li><a href="#org1019362">3.1. Type</a></li>
<li><a href="#org2371d45">3.2. Access</a></li>
<li><a href="#org9169380">3.3. Creation</a></li>
<li><a href="#orgadedc00">3.4. Printers</a></li>
<li><a href="#orgd59f48c">3.1. Type</a></li>
<li><a href="#org044c217">3.2. Access</a></li>
<li><a href="#org6a9efbf">3.3. Creation</a></li>
<li><a href="#orgcabf1a1">3.4. Printers</a></li>
</ul>
</li>
<li><a href="#org750192c">4. Atomic shell pair</a>
<li><a href="#org6e4ac83">4. Atomic shell pair</a>
<ul>
<li><a href="#org6b2bebd">4.1. Type</a></li>
<li><a href="#org0967ce4">4.2. Access</a></li>
<li><a href="#org176c31a">4.3. Creation</a></li>
<li><a href="#org3f5a744">4.4. Printers</a></li>
<li><a href="#org9a03038">4.1. Type</a></li>
<li><a href="#org9072da8">4.2. Access</a></li>
<li><a href="#orgf7291bd">4.3. Creation</a></li>
<li><a href="#orge4f55f1">4.4. Printers</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-orgf3ada33" class="outline-2">
<h2 id="orgf3ada33"><span class="section-number-2">1</span> Summmary</h2>
<div id="outline-container-org458f6db" class="outline-2">
<h2 id="org458f6db"><span class="section-number-2">1</span> Summary</h2>
</div>
<div id="outline-container-org7457529" class="outline-2">
<h2 id="org7457529"><span class="section-number-2">2</span> Atomic shell</h2>
<div id="outline-container-org000b493" class="outline-2">
<h2 id="org000b493"><span class="section-number-2">2</span> Atomic shell</h2>
<div class="outline-text-2" id="text-2">
<p>
Set of contracted Gaussians differing only by the powers of \(x\), \(y\) and \(z\), with a
@ -339,8 +339,8 @@ particular powers of \(x,y,z\) (<code>PrimitiveShell.norm_coef_scale</code>)</li
</div>
<div id="outline-container-org0e4fe4d" class="outline-3">
<h3 id="org0e4fe4d"><span class="section-number-3">2.1</span> Type</h3>
<div id="outline-container-orgd5a7f6d" class="outline-3">
<h3 id="orgd5a7f6d"><span class="section-number-3">2.1</span> Type</h3>
<div class="outline-text-3" id="text-2-1">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span>
@ -351,8 +351,8 @@ particular powers of \(x,y,z\) (<code>PrimitiveShell.norm_coef_scale</code>)</li
</div>
</div>
<div id="outline-container-orgde1bce4" class="outline-3">
<h3 id="orgde1bce4"><span class="section-number-3">2.2</span> Access</h3>
<div id="outline-container-org3d580ec" class="outline-3">
<h3 id="org3d580ec"><span class="section-number-3">2.2</span> Access</h3>
<div class="outline-text-3" id="text-2-2">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">ang_mom</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Angular_momentum.</span>t
@ -429,14 +429,14 @@ particular powers of \(x,y,z\) (<code>PrimitiveShell.norm_coef_scale</code>)</li
</tbody>
</table>
<pre class="example" id="org37e8ada">
<pre class="example" id="org1efe2a1">
</pre>
</div>
</div>
<div id="outline-container-org24b2b8e" class="outline-3">
<h3 id="org24b2b8e"><span class="section-number-3">2.3</span> Creation</h3>
<div id="outline-container-org2a3c76d" class="outline-3">
<h3 id="org2a3c76d"><span class="section-number-3">2.3</span> Creation</h3>
<div class="outline-text-3" id="text-2-3">
<div class="org-src-container">
<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">?index</span><span class="org-tuareg-font-lock-operator">:</span>int <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Contracted_shell.</span>t array <span class="org-tuareg-font-lock-operator">-&gt;</span> t
@ -468,8 +468,8 @@ particular powers of \(x,y,z\) (<code>PrimitiveShell.norm_coef_scale</code>)</li
</div>
</div>
<div id="outline-container-orge729f26" class="outline-3">
<h3 id="orge729f26"><span class="section-number-3">2.4</span> Printers</h3>
<div id="outline-container-orge3b7bbf" class="outline-3">
<h3 id="orge3b7bbf"><span class="section-number-3">2.4</span> Printers</h3>
<div class="outline-text-3" id="text-2-4">
<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">-&gt;</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> unit
@ -479,8 +479,8 @@ particular powers of \(x,y,z\) (<code>PrimitiveShell.norm_coef_scale</code>)</li
</div>
</div>
<div id="outline-container-org8871eba" class="outline-2">
<h2 id="org8871eba"><span class="section-number-2">3</span> Atomic shell pair couple</h2>
<div id="outline-container-org403784b" class="outline-2">
<h2 id="org403784b"><span class="section-number-2">3</span> Atomic shell pair couple</h2>
<div class="outline-text-2" id="text-3">
<p>
An atomic shell pair couple is the cartesian product between two sets of functions, one
@ -496,8 +496,8 @@ acting on different electrons, since they will be coupled by a two-electron oper
</div>
<div id="outline-container-org1019362" class="outline-3">
<h3 id="org1019362"><span class="section-number-3">3.1</span> Type</h3>
<div id="outline-container-orgd59f48c" class="outline-3">
<h3 id="orgd59f48c"><span class="section-number-3">3.1</span> Type</h3>
<div class="outline-text-3" id="text-3-1">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span>
@ -508,8 +508,8 @@ acting on different electrons, since they will be coupled by a two-electron oper
</div>
</div>
<div id="outline-container-org2371d45" class="outline-3">
<h3 id="org2371d45"><span class="section-number-3">3.2</span> Access</h3>
<div id="outline-container-org044c217" class="outline-3">
<h3 id="org044c217"><span class="section-number-3">3.2</span> Access</h3>
<div class="outline-text-3" id="text-3-2">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">ang_mom</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Angular_momentum.</span>t
@ -594,8 +594,8 @@ acting on different electrons, since they will be coupled by a two-electron oper
</div>
</div>
<div id="outline-container-org9169380" class="outline-3">
<h3 id="org9169380"><span class="section-number-3">3.3</span> Creation</h3>
<div id="outline-container-org6a9efbf" class="outline-3">
<h3 id="org6a9efbf"><span class="section-number-3">3.3</span> Creation</h3>
<div class="outline-text-3" id="text-3-3">
<div class="org-src-container">
<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">?cutoff</span><span class="org-tuareg-font-lock-operator">:</span>float <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Atomic_shell_pair.</span>t <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Atomic_shell_pair.</span>t <span class="org-tuareg-font-lock-operator">-&gt;</span> t option
@ -621,14 +621,14 @@ Default cutoff is \(\epsilon\).
</tbody>
</table>
<pre class="example" id="org6444454">
<pre class="example" id="org406c3a5">
</pre>
</div>
</div>
<div id="outline-container-orgadedc00" class="outline-3">
<h3 id="orgadedc00"><span class="section-number-3">3.4</span> Printers</h3>
<div id="outline-container-orgcabf1a1" class="outline-3">
<h3 id="orgcabf1a1"><span class="section-number-3">3.4</span> Printers</h3>
<div class="outline-text-3" id="text-3-4">
<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">-&gt;</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> unit
@ -638,8 +638,8 @@ Default cutoff is \(\epsilon\).
</div>
</div>
<div id="outline-container-org750192c" class="outline-2">
<h2 id="org750192c"><span class="section-number-2">4</span> Atomic shell pair</h2>
<div id="outline-container-org6e4ac83" class="outline-2">
<h2 id="org6e4ac83"><span class="section-number-2">4</span> Atomic shell pair</h2>
<div class="outline-text-2" id="text-4">
<p>
Data structure to represent pairs of atomic shells. The products of
@ -651,8 +651,8 @@ An atomic shell pair is an array of pairs of contracted shells.
</p>
</div>
<div id="outline-container-org6b2bebd" class="outline-3">
<h3 id="org6b2bebd"><span class="section-number-3">4.1</span> Type</h3>
<div id="outline-container-org9a03038" class="outline-3">
<h3 id="org9a03038"><span class="section-number-3">4.1</span> Type</h3>
<div class="outline-text-3" id="text-4-1">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span>
@ -663,8 +663,8 @@ An atomic shell pair is an array of pairs of contracted shells.
</div>
</div>
<div id="outline-container-org0967ce4" class="outline-3">
<h3 id="org0967ce4"><span class="section-number-3">4.2</span> Access</h3>
<div id="outline-container-org9072da8" class="outline-3">
<h3 id="org9072da8"><span class="section-number-3">4.2</span> Access</h3>
<div class="outline-text-3" id="text-4-2">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">atomic_shell_a</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Atomic_shell.</span>t
@ -731,8 +731,8 @@ An atomic shell pair is an array of pairs of contracted shells.
</div>
</div>
<div id="outline-container-org176c31a" class="outline-3">
<h3 id="org176c31a"><span class="section-number-3">4.3</span> Creation</h3>
<div id="outline-container-orgf7291bd" class="outline-3">
<h3 id="orgf7291bd"><span class="section-number-3">4.3</span> Creation</h3>
<div class="outline-text-3" id="text-4-3">
<div class="org-src-container">
<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">?cutoff</span><span class="org-tuareg-font-lock-operator">:</span>float <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Atomic_shell.</span>t <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Atomic_shell.</span>t <span class="org-tuareg-font-lock-operator">-&gt;</span> t option
@ -765,8 +765,8 @@ If an atomic shell pair is not significant, sets the value to <code>None</code>.
</div>
</div>
<div id="outline-container-org3f5a744" class="outline-3">
<h3 id="org3f5a744"><span class="section-number-3">4.4</span> Printers</h3>
<div id="outline-container-orge4f55f1" class="outline-3">
<h3 id="orge4f55f1"><span class="section-number-3">4.4</span> Printers</h3>
<div class="outline-text-3" id="text-4-4">
<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">-&gt;</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> unit
@ -778,7 +778,7 @@ If an atomic shell pair is not significant, sets the value to <code>None</code>.
</div>
<div id="postamble" class="status">
<p class="author">Author: Anthony Scemama</p>
<p class="date">Created: 2021-01-27 Wed 23:44</p>
<p class="date">Created: 2021-10-19 Tue 16:20</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

10
docs/gaussian_integrals.html
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@ -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>
<!-- 2021-01-27 Wed 23:44 -->
<!-- 2021-10-19 Tue 16:20 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Gaussian integrals</title>
@ -250,18 +250,18 @@ org_html_manager.setup(); // activate after the parameters are set
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orge4d21a1">1. Summmary</a></li>
<li><a href="#org3f35417">1. Summary</a></li>
</ul>
</div>
</div>
<div id="outline-container-orge4d21a1" class="outline-2">
<h2 id="orge4d21a1"><span class="section-number-2">1</span> Summmary</h2>
<div id="outline-container-org3f35417" class="outline-2">
<h2 id="org3f35417"><span class="section-number-2">1</span> Summary</h2>
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: Anthony Scemama</p>
<p class="date">Created: 2021-01-27 Wed 23:44</p>
<p class="date">Created: 2021-10-19 Tue 16:20</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

10
docs/linear_algebra.html
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@ -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>
<!-- 2021-01-29 Fri 15:35 -->
<!-- 2021-10-19 Tue 16:20 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Linear Algebra</title>
@ -250,18 +250,18 @@ org_html_manager.setup(); // activate after the parameters are set
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org73480ff">1. Summmary</a></li>
<li><a href="#org4e0185b">1. Summary</a></li>
</ul>
</div>
</div>
<div id="outline-container-org73480ff" class="outline-2">
<h2 id="org73480ff"><span class="section-number-2">1</span> Summmary</h2>
<div id="outline-container-org4e0185b" class="outline-2">
<h2 id="org4e0185b"><span class="section-number-2">1</span> Summary</h2>
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: Anthony Scemama</p>
<p class="date">Created: 2021-01-29 Fri 15:35</p>
<p class="date">Created: 2021-10-19 Tue 16:20</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

90
docs/mo.html
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@ -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>
<!-- 2021-02-03 Wed 10:47 -->
<!-- 2021-10-19 Tue 16:20 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Molecular orbitals</title>
@ -272,46 +272,46 @@ org_html_manager.setup(); // activate after the parameters are set
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org16f6c6b">1. Summmary</a></li>
<li><a href="#orgebbcfe0">2. Frozen core</a>
<li><a href="#org67a6ab4">1. Summary</a></li>
<li><a href="#org534e8e0">2. Frozen core</a>
<ul>
<li><a href="#org61f3b2e">2.1. Type</a></li>
<li><a href="#orgfff2d7e">2.2. Creation</a></li>
<li><a href="#org2519af7">2.3. Access</a></li>
<li><a href="#orga5fe616">2.4. Printers</a></li>
<li><a href="#org5cdd86a">2.1. Type</a></li>
<li><a href="#orga19472c">2.2. Creation</a></li>
<li><a href="#org19a22fb">2.3. Access</a></li>
<li><a href="#org276b149">2.4. Printers</a></li>
</ul>
</li>
<li><a href="#org03637a8">3. Orbital localization</a>
<li><a href="#org3963dec">3. Orbital localization</a>
<ul>
<li><a href="#orge723841">3.1. Type</a></li>
<li><a href="#org6933918">3.2. Edmiston-Rudenberg</a></li>
<li><a href="#org44c9408">3.3. Boys</a></li>
<li><a href="#org64dada8">3.4. Access</a></li>
<li><a href="#org5b86753">3.5. Printers</a></li>
<li><a href="#orgcfa3655">3.6. Tests</a></li>
<li><a href="#org14e39a2">3.1. Type</a></li>
<li><a href="#orgd0f2a90">3.2. Edmiston-Rudenberg</a></li>
<li><a href="#orga75e980">3.3. Boys</a></li>
<li><a href="#org6f32371">3.4. Access</a></li>
<li><a href="#org10eb2b8">3.5. Printers</a></li>
<li><a href="#org3024ac7">3.6. Tests</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org16f6c6b" class="outline-2">
<h2 id="org16f6c6b"><span class="section-number-2">1</span> Summmary</h2>
<div id="outline-container-org67a6ab4" class="outline-2">
<h2 id="org67a6ab4"><span class="section-number-2">1</span> Summary</h2>
</div>
<div id="outline-container-orgebbcfe0" class="outline-2">
<h2 id="orgebbcfe0"><span class="section-number-2">2</span> Frozen core</h2>
<div id="outline-container-org534e8e0" class="outline-2">
<h2 id="org534e8e0"><span class="section-number-2">2</span> Frozen core</h2>
<div class="outline-text-2" id="text-2">
<p>
Defines how the core electrons are frozen, for each atom.
</p>
</div>
<div id="outline-container-org61f3b2e" class="outline-3">
<h3 id="org61f3b2e"><span class="section-number-3">2.1</span> Type</h3>
<div id="outline-container-org5cdd86a" class="outline-3">
<h3 id="org5cdd86a"><span class="section-number-3">2.1</span> Type</h3>
<div class="outline-text-3" id="text-2-1">
<div class="org-src-container">
<pre class="src src-ocaml" id="org786e5f6"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">kind</span> <span class="org-tuareg-font-lock-operator">=</span>
<pre class="src src-ocaml" id="orgd878327"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">kind</span> <span class="org-tuareg-font-lock-operator">=</span>
<span class="org-tuareg-font-lock-operator">|</span> <span class="org-tuareg-font-lock-constructor">All_electron</span>
<span class="org-tuareg-font-lock-operator">|</span> <span class="org-tuareg-font-lock-constructor">Small</span>
<span class="org-tuareg-font-lock-operator">|</span> Large
@ -325,8 +325,8 @@ Defines how the core electrons are frozen, for each atom.
</div>
</div>
<div id="outline-container-orgfff2d7e" class="outline-3">
<h3 id="orgfff2d7e"><span class="section-number-3">2.2</span> Creation</h3>
<div id="outline-container-orga19472c" class="outline-3">
<h3 id="orga19472c"><span class="section-number-3">2.2</span> Creation</h3>
<div class="outline-text-3" id="text-2-2">
<div class="org-src-container">
<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> kind <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Particles.Nuclei.</span>t <span class="org-tuareg-font-lock-operator">-&gt;</span> t
@ -362,7 +362,7 @@ Defines how the core electrons are frozen, for each atom.
</tbody>
</table>
<pre class="example" id="org863654b">
<pre class="example" id="org74f6971">
let f = Frozen_core.(make Small nuclei) ;;
val f : Frozen_core.t = [|0; 2; 2; 0|]
@ -372,8 +372,8 @@ val f : Frozen_core.t = [|0; 2; 2; 0|]
</div>
</div>
<div id="outline-container-org2519af7" class="outline-3">
<h3 id="org2519af7"><span class="section-number-3">2.3</span> Access</h3>
<div id="outline-container-org19a22fb" class="outline-3">
<h3 id="org19a22fb"><span class="section-number-3">2.3</span> Access</h3>
<div class="outline-text-3" id="text-2-3">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">num_elec</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> int
@ -402,7 +402,7 @@ val f : Frozen_core.t = [|0; 2; 2; 0|]
</tbody>
</table>
<pre class="example" id="org517ff86">
<pre class="example" id="org7ed9c90">
Frozen_core.num_elec f ;;
- : int = 4
@ -412,8 +412,8 @@ Frozen_core.num_mos f ;;
</div>
</div>
<div id="outline-container-orga5fe616" class="outline-3">
<h3 id="orga5fe616"><span class="section-number-3">2.4</span> Printers</h3>
<div id="outline-container-org276b149" class="outline-3">
<h3 id="org276b149"><span class="section-number-3">2.4</span> Printers</h3>
<div class="outline-text-3" id="text-2-4">
<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">-&gt;</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> unit
@ -423,8 +423,8 @@ Frozen_core.num_mos f ;;
</div>
</div>
<div id="outline-container-org03637a8" class="outline-2">
<h2 id="org03637a8"><span class="section-number-2">3</span> Orbital localization</h2>
<div id="outline-container-org3963dec" class="outline-2">
<h2 id="org3963dec"><span class="section-number-2">3</span> Orbital localization</h2>
<div class="outline-text-2" id="text-3">
<p>
Molecular orbital localization function.
@ -440,11 +440,11 @@ Edmiston-Rudenberg:
</div>
<div id="outline-container-orge723841" class="outline-3">
<h3 id="orge723841"><span class="section-number-3">3.1</span> Type</h3>
<div id="outline-container-org14e39a2" class="outline-3">
<h3 id="org14e39a2"><span class="section-number-3">3.1</span> Type</h3>
<div class="outline-text-3" id="text-3-1">
<div class="org-src-container">
<pre class="src src-ocaml" id="org1b6afe0"><span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Linear_algebra</span>
<pre class="src src-ocaml" id="org06f9604"><span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Linear_algebra</span>
<span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">localization_kind</span> <span class="org-tuareg-font-lock-operator">=</span>
<span class="org-tuareg-font-lock-operator">|</span> <span class="org-tuareg-font-lock-constructor">Edmiston</span>
@ -464,16 +464,16 @@ Edmiston-Rudenberg:
</div>
</div>
<div id="outline-container-org6933918" class="outline-3">
<h3 id="org6933918"><span class="section-number-3">3.2</span> Edmiston-Rudenberg</h3>
<div id="outline-container-orgd0f2a90" class="outline-3">
<h3 id="orgd0f2a90"><span class="section-number-3">3.2</span> Edmiston-Rudenberg</h3>
</div>
<div id="outline-container-org44c9408" class="outline-3">
<h3 id="org44c9408"><span class="section-number-3">3.3</span> Boys</h3>
<div id="outline-container-orga75e980" class="outline-3">
<h3 id="orga75e980"><span class="section-number-3">3.3</span> Boys</h3>
</div>
<div id="outline-container-org64dada8" class="outline-3">
<h3 id="org64dada8"><span class="section-number-3">3.4</span> Access</h3>
<div id="outline-container-org6f32371" class="outline-3">
<h3 id="org6f32371"><span class="section-number-3">3.4</span> Access</h3>
<div class="outline-text-3" id="text-3-4">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">kind</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> localization_kind
@ -522,8 +522,8 @@ Edmiston-Rudenberg:
</div>
</div>
<div id="outline-container-org5b86753" class="outline-3">
<h3 id="org5b86753"><span class="section-number-3">3.5</span> Printers</h3>
<div id="outline-container-org10eb2b8" class="outline-3">
<h3 id="org10eb2b8"><span class="section-number-3">3.5</span> Printers</h3>
<div class="outline-text-3" id="text-3-5">
<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">-&gt;</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> unit
@ -532,14 +532,14 @@ Edmiston-Rudenberg:
</div>
</div>
<div id="outline-container-orgcfa3655" class="outline-3">
<h3 id="orgcfa3655"><span class="section-number-3">3.6</span> Tests</h3>
<div id="outline-container-org3024ac7" class="outline-3">
<h3 id="org3024ac7"><span class="section-number-3">3.6</span> Tests</h3>
</div>
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: Anthony Scemama</p>
<p class="date">Created: 2021-02-03 Wed 10:47</p>
<p class="date">Created: 2021-10-19 Tue 16:20</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

178
docs/particles.html
View File

@ -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>
<!-- 2021-01-27 Wed 23:44 -->
<!-- 2021-10-19 Tue 16:20 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Common</title>
@ -272,75 +272,75 @@ org_html_manager.setup(); // activate after the parameters are set
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgc3aa2b1">1. Summmary</a></li>
<li><a href="#orgf4a663e">2. Electrons</a>
<li><a href="#org16377b0">1. Summary</a></li>
<li><a href="#orga526d51">2. Electrons</a>
<ul>
<li><a href="#org88e7967">2.1. Type</a></li>
<li><a href="#org376ca80">2.2. Creation</a></li>
<li><a href="#orgd1d110c">2.3. Access</a></li>
<li><a href="#org1d2a3d7">2.4. Printers</a></li>
<li><a href="#org7b61e24">2.5. Tests</a></li>
<li><a href="#org0f89435">2.1. Type</a></li>
<li><a href="#org19a0b2f">2.2. Creation</a></li>
<li><a href="#orge91e3a6">2.3. Access</a></li>
<li><a href="#orgda16d90">2.4. Printers</a></li>
<li><a href="#orgfd02552">2.5. Tests</a></li>
</ul>
</li>
<li><a href="#org918ae65">3. Element</a>
<li><a href="#org725a06a">3. Element</a>
<ul>
<li><a href="#org8889a68">3.1. Type</a></li>
<li><a href="#orgc639e8c">3.2. Conversion</a></li>
<li><a href="#org8706da1">3.3. Database information</a></li>
<li><a href="#org95418b5">3.4. Printers</a></li>
<li><a href="#orgcb66a4e">3.1. Type</a></li>
<li><a href="#org69ad620">3.2. Conversion</a></li>
<li><a href="#orge6b6575">3.3. Database information</a></li>
<li><a href="#orgb858483">3.4. Printers</a></li>
</ul>
</li>
<li><a href="#orgc544cb3">4. Atomic mass</a></li>
<li><a href="#org0dcc52f">5. Nuclei</a>
<li><a href="#orgd76ed1c">4. Atomic mass</a></li>
<li><a href="#orgc35a790">5. Nuclei</a>
<ul>
<li><a href="#org83b7fcb">5.1. Type</a></li>
<li><a href="#orgcba845a">5.2. xyz file lexer/parser</a>
<li><a href="#org171da4c">5.1. Type</a></li>
<li><a href="#orge62900d">5.2. xyz file lexer/parser</a>
<ul>
<li><a href="#org196ee2a">5.2.1. Lexer</a></li>
<li><a href="#orgda1a58a">5.2.2. Parser</a></li>
<li><a href="#orgd09795d">5.2.1. Lexer</a></li>
<li><a href="#orgba2987d">5.2.2. Parser</a></li>
</ul>
</li>
<li><a href="#org4bc334a">5.3. Conversion</a></li>
<li><a href="#org259e4f9">5.4. <span class="todo TODO">TODO</span> Query</a></li>
<li><a href="#org606af7e">5.5. Printers</a></li>
<li><a href="#orgcd3169c">5.6. Tests</a></li>
<li><a href="#orgf02e81a">5.3. Conversion</a></li>
<li><a href="#orgc2f2524">5.4. <span class="todo TODO">TODO</span> Query</a></li>
<li><a href="#orgfd12c55">5.5. Printers</a></li>
<li><a href="#org4030958">5.6. Tests</a></li>
</ul>
</li>
<li><a href="#orgf9d75ec">6. Z-matrix</a>
<li><a href="#org278d5c2">6. Z-matrix</a>
<ul>
<li><a href="#org2ee988d">6.1. Type</a></li>
<li><a href="#org0a2b5eb">6.2. Conversion</a></li>
<li><a href="#org36acab9">6.3. Printers</a></li>
<li><a href="#org4594ad5">6.1. Type</a></li>
<li><a href="#org917cb80">6.2. Conversion</a></li>
<li><a href="#orge01b8a9">6.3. Printers</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-orgc3aa2b1" class="outline-2">
<h2 id="orgc3aa2b1"><span class="section-number-2">1</span> Summmary</h2>
<div id="outline-container-org16377b0" class="outline-2">
<h2 id="org16377b0"><span class="section-number-2">1</span> Summary</h2>
</div>
<div id="outline-container-orgf4a663e" class="outline-2">
<h2 id="orgf4a663e"><span class="section-number-2">2</span> Electrons</h2>
<div id="outline-container-orga526d51" class="outline-2">
<h2 id="orga526d51"><span class="section-number-2">2</span> Electrons</h2>
<div class="outline-text-2" id="text-2">
<p>
Data structure which contains the number of &alpha; and &beta; electrons.
</p>
</div>
<div id="outline-container-org88e7967" class="outline-3">
<h3 id="org88e7967"><span class="section-number-3">2.1</span> Type</h3>
<div id="outline-container-org0f89435" class="outline-3">
<h3 id="org0f89435"><span class="section-number-3">2.1</span> Type</h3>
<div class="outline-text-3" id="text-2-1">
<div class="org-src-container">
<pre class="src src-ocaml" id="org380f263"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span>
<pre class="src src-ocaml" id="org49290f9"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span>
</pre>
</div>
</div>
</div>
<div id="outline-container-org376ca80" class="outline-3">
<h3 id="org376ca80"><span class="section-number-3">2.2</span> Creation</h3>
<div id="outline-container-org19a0b2f" class="outline-3">
<h3 id="org19a0b2f"><span class="section-number-3">2.2</span> Creation</h3>
<div class="outline-text-3" id="text-2-2">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Common</span>
@ -372,15 +372,15 @@ Data structure which contains the number of &alpha; and &beta; electrons.
<tr>
<td class="org-left"><code>of_atoms</code></td>
<td class="org-left">Creates the data relative to electrons for a molecular system described by <a href="#org117d80f"><code>Nuclei.t</code></a> for a given total charge and spin multiplicity.</td>
<td class="org-left">Creates the data relative to electrons for a molecular system described by <a href="#org206e0b6"><code>Nuclei.t</code></a> for a given total charge and spin multiplicity.</td>
</tr>
</tbody>
</table>
</div>
</div>
<div id="outline-container-orgd1d110c" class="outline-3">
<h3 id="orgd1d110c"><span class="section-number-3">2.3</span> Access</h3>
<div id="outline-container-orge91e3a6" class="outline-3">
<h3 id="orge91e3a6"><span class="section-number-3">2.3</span> Access</h3>
<div class="outline-text-3" id="text-2-3">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">charge</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Charge.</span>t
@ -429,8 +429,8 @@ Data structure which contains the number of &alpha; and &beta; electrons.
</div>
</div>
<div id="outline-container-org1d2a3d7" class="outline-3">
<h3 id="org1d2a3d7"><span class="section-number-3">2.4</span> Printers</h3>
<div id="outline-container-orgda16d90" class="outline-3">
<h3 id="orgda16d90"><span class="section-number-3">2.4</span> Printers</h3>
<div class="outline-text-3" id="text-2-4">
<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">-&gt;</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> unit
@ -439,24 +439,24 @@ Data structure which contains the number of &alpha; and &beta; electrons.
</div>
</div>
<div id="outline-container-org7b61e24" class="outline-3">
<h3 id="org7b61e24"><span class="section-number-3">2.5</span> Tests</h3>
<div id="outline-container-orgfd02552" class="outline-3">
<h3 id="orgfd02552"><span class="section-number-3">2.5</span> Tests</h3>
</div>
</div>
<div id="outline-container-org918ae65" class="outline-2">
<h2 id="org918ae65"><span class="section-number-2">3</span> Element</h2>
<div id="outline-container-org725a06a" class="outline-2">
<h2 id="org725a06a"><span class="section-number-2">3</span> Element</h2>
<div class="outline-text-2" id="text-3">
<p>
Chemical elements.
</p>
</div>
<div id="outline-container-org8889a68" class="outline-3">
<h3 id="org8889a68"><span class="section-number-3">3.1</span> Type</h3>
<div id="outline-container-orgcb66a4e" class="outline-3">
<h3 id="orgcb66a4e"><span class="section-number-3">3.1</span> Type</h3>
<div class="outline-text-3" id="text-3-1">
<div class="org-src-container">
<pre class="src src-ocaml" id="org2343857"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span> <span class="org-tuareg-font-lock-operator">=</span>
<pre class="src src-ocaml" id="orgd93555e"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span> <span class="org-tuareg-font-lock-operator">=</span>
<span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">X</span>
<span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">H</span> <span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">He</span>
<span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Li</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Be</span> <span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">B</span> <span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">C</span> <span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">N</span> <span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">O</span> <span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">F</span> <span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Ne</span>
@ -473,8 +473,8 @@ Chemical elements.
</div>
</div>
<div id="outline-container-orgc639e8c" class="outline-3">
<h3 id="orgc639e8c"><span class="section-number-3">3.2</span> Conversion</h3>
<div id="outline-container-org69ad620" class="outline-3">
<h3 id="org69ad620"><span class="section-number-3">3.2</span> Conversion</h3>
<div class="outline-text-3" id="text-3-2">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">of_string</span> <span class="org-tuareg-font-lock-operator">:</span> string <span class="org-tuareg-font-lock-operator">-&gt;</span> t
@ -535,7 +535,7 @@ Chemical elements.
</tbody>
</table>
<pre class="example" id="orgce999ba">
<pre class="example" id="orge0cc4ce">
Element.of_string "Fe" ;;
- : Element.t = Particles.Element.Fe
@ -554,8 +554,8 @@ Element.(to_string Fe);;
</div>
</div>
<div id="outline-container-org8706da1" class="outline-3">
<h3 id="org8706da1"><span class="section-number-3">3.3</span> Database information</h3>
<div id="outline-container-orge6b6575" class="outline-3">
<h3 id="orge6b6575"><span class="section-number-3">3.3</span> Database information</h3>
<div class="outline-text-3" id="text-3-3">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">covalent_radius</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Non_negative_float.</span>t
@ -604,8 +604,8 @@ Element.(to_string Fe);;
</div>
</div>
<div id="outline-container-org95418b5" class="outline-3">
<h3 id="org95418b5"><span class="section-number-3">3.4</span> Printers</h3>
<div id="outline-container-orgb858483" class="outline-3">
<h3 id="orgb858483"><span class="section-number-3">3.4</span> Printers</h3>
<div class="outline-text-3" id="text-3-4">
<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">-&gt;</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> unit
@ -616,34 +616,34 @@ Element.(to_string Fe);;
</div>
</div>
<div id="outline-container-orgc544cb3" class="outline-2">
<h2 id="orgc544cb3"><span class="section-number-2">4</span> Atomic mass</h2>
<div id="outline-container-orgd76ed1c" class="outline-2">
<h2 id="orgd76ed1c"><span class="section-number-2">4</span> Atomic mass</h2>
<div class="outline-text-2" id="text-4">
<p>
Atomic mass, a non-negative float.
</p>
<div class="org-src-container">
<pre class="src src-ocaml" id="orgb21935a"><span class="org-tuareg-font-lock-governing">include</span> <span class="org-tuareg-font-lock-governing">module type of</span> <span class="org-tuareg-font-lock-module">Common.Non_negative_float</span>
<pre class="src src-ocaml" id="orgba2cdaa"><span class="org-tuareg-font-lock-governing">include</span> <span class="org-tuareg-font-lock-governing">module type of</span> <span class="org-tuareg-font-lock-module">Common.Non_negative_float</span>
</pre>
</div>
</div>
</div>
<div id="outline-container-org0dcc52f" class="outline-2">
<h2 id="org0dcc52f"><span class="section-number-2">5</span> Nuclei</h2>
<div id="outline-container-orgc35a790" class="outline-2">
<h2 id="orgc35a790"><span class="section-number-2">5</span> Nuclei</h2>
<div class="outline-text-2" id="text-5">
</div>
<div id="outline-container-org83b7fcb" class="outline-3">
<h3 id="org83b7fcb"><span class="section-number-3">5.1</span> Type</h3>
<div id="outline-container-org171da4c" class="outline-3">
<h3 id="org171da4c"><span class="section-number-3">5.1</span> Type</h3>
<div class="outline-text-3" id="text-5-1">
<p>
<a id="org117d80f"><code>Nuclei.t</code></a>
<a id="org206e0b6"><code>Nuclei.t</code></a>
</p>
<div class="org-src-container">
<pre class="src src-ocaml" id="org9b85d6c"><span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Common</span>
<pre class="src src-ocaml" id="orgb9e1e3d"><span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Common</span>
<span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span> <span class="org-tuareg-font-lock-operator">=</span> <span class="org-tuareg-font-lock-operator">(</span><span class="org-tuareg-font-lock-module">Element.</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> array
</pre>
@ -651,12 +651,12 @@ Atomic mass, a non-negative float.
</div>
</div>
<div id="outline-container-orgcba845a" class="outline-3">
<h3 id="orgcba845a"><span class="section-number-3">5.2</span> xyz file lexer/parser</h3>
<div id="outline-container-orge62900d" class="outline-3">
<h3 id="orge62900d"><span class="section-number-3">5.2</span> xyz file lexer/parser</h3>
<div class="outline-text-3" id="text-5-2">
</div>
<div id="outline-container-org196ee2a" class="outline-4">
<h4 id="org196ee2a"><span class="section-number-4">5.2.1</span> Lexer</h4>
<div id="outline-container-orgd09795d" class="outline-4">
<h4 id="orgd09795d"><span class="section-number-4">5.2.1</span> Lexer</h4>
<div class="outline-text-4" id="text-5-2-1">
<p>
<code>nuclei_lexer.mll</code> contains the description of the lexemes used in
@ -709,8 +709,8 @@ rule read_all <span class="org-tuareg-font-lock-operator">=</span> parse
</div>
</div>
<div id="outline-container-orgda1a58a" class="outline-4">
<h4 id="orgda1a58a"><span class="section-number-4">5.2.2</span> Parser</h4>
<div id="outline-container-orgba2987d" class="outline-4">
<h4 id="orgba2987d"><span class="section-number-4">5.2.2</span> Parser</h4>
<div class="outline-text-4" id="text-5-2-2">
<p>
<code>xyz_parser.mly</code> parses nuclear coordinates in xyz format.
@ -829,8 +829,8 @@ an <code>xyz_file</code> data structure.
</div>
</div>
<div id="outline-container-org4bc334a" class="outline-3">
<h3 id="org4bc334a"><span class="section-number-3">5.3</span> Conversion</h3>
<div id="outline-container-orgf02e81a" class="outline-3">
<h3 id="orgf02e81a"><span class="section-number-3">5.3</span> Conversion</h3>
<div class="outline-text-3" id="text-5-3">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">of_xyz_string</span> <span class="org-tuareg-font-lock-operator">:</span> string <span class="org-tuareg-font-lock-operator">-&gt;</span> t
@ -889,8 +889,8 @@ an <code>xyz_file</code> data structure.
</div>
</div>
<div id="outline-container-org259e4f9" class="outline-3">
<h3 id="org259e4f9"><span class="section-number-3">5.4</span> <span class="todo TODO">TODO</span> Query</h3>
<div id="outline-container-orgc2f2524" class="outline-3">
<h3 id="orgc2f2524"><span class="section-number-3">5.4</span> <span class="todo TODO">TODO</span> Query</h3>
<div class="outline-text-3" id="text-5-4">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">formula</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> string
@ -939,8 +939,8 @@ an <code>xyz_file</code> data structure.
</div>
</div>
<div id="outline-container-org606af7e" class="outline-3">
<h3 id="org606af7e"><span class="section-number-3">5.5</span> Printers</h3>
<div id="outline-container-orgfd12c55" class="outline-3">
<h3 id="orgfd12c55"><span class="section-number-3">5.5</span> Printers</h3>
<div class="outline-text-3" id="text-5-5">
<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">-&gt;</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> unit
@ -949,31 +949,31 @@ an <code>xyz_file</code> data structure.
</div>
</div>
<div id="outline-container-orgcd3169c" class="outline-3">
<h3 id="orgcd3169c"><span class="section-number-3">5.6</span> Tests</h3>
<div id="outline-container-org4030958" class="outline-3">
<h3 id="org4030958"><span class="section-number-3">5.6</span> Tests</h3>
</div>
</div>
<div id="outline-container-orgf9d75ec" class="outline-2">
<h2 id="orgf9d75ec"><span class="section-number-2">6</span> Z-matrix</h2>
<div id="outline-container-org278d5c2" class="outline-2">
<h2 id="org278d5c2"><span class="section-number-2">6</span> Z-matrix</h2>
<div class="outline-text-2" id="text-6">
<p>
Z-matrix representation of nuclear coordinates.
</p>
</div>
<div id="outline-container-org2ee988d" class="outline-3">
<h3 id="org2ee988d"><span class="section-number-3">6.1</span> Type</h3>
<div id="outline-container-org4594ad5" class="outline-3">
<h3 id="org4594ad5"><span class="section-number-3">6.1</span> Type</h3>
<div class="outline-text-3" id="text-6-1">
<div class="org-src-container">
<pre class="src src-ocaml" id="org2500b30"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span>
<pre class="src src-ocaml" id="org7586df6"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span>
</pre>
</div>
</div>
</div>
<div id="outline-container-org0a2b5eb" class="outline-3">
<h3 id="org0a2b5eb"><span class="section-number-3">6.2</span> Conversion</h3>
<div id="outline-container-org917cb80" class="outline-3">
<h3 id="org917cb80"><span class="section-number-3">6.2</span> Conversion</h3>
<div class="outline-text-3" id="text-6-2">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">of_string</span> <span class="org-tuareg-font-lock-operator">:</span> string <span class="org-tuareg-font-lock-operator">-&gt;</span> t
@ -1008,7 +1008,7 @@ Z-matrix representation of nuclear coordinates.
</tbody>
</table>
<pre class="example" id="org4442d9d">
<pre class="example" id="org8bd7049">
let zmt = Zmatrix.of_string "
n
n 1 nn
@ -1053,8 +1053,8 @@ H -0.568803 -0.793910 1.726048"
</div>
<div id="outline-container-org36acab9" class="outline-3">
<h3 id="org36acab9"><span class="section-number-3">6.3</span> Printers</h3>
<div id="outline-container-orge01b8a9" class="outline-3">
<h3 id="orge01b8a9"><span class="section-number-3">6.3</span> Printers</h3>
<div class="outline-text-3" id="text-6-3">
<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">-&gt;</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> unit
@ -1066,7 +1066,7 @@ H -0.568803 -0.793910 1.726048"
</div>
<div id="postamble" class="status">
<p class="author">Author: Anthony Scemama</p>
<p class="date">Created: 2021-01-27 Wed 23:44</p>
<p class="date">Created: 2021-10-19 Tue 16:20</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

50
docs/perturbation.html
View File

@ -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>
<!-- 2021-01-27 Wed 23:44 -->
<!-- 2021-10-19 Tue 16:20 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Perturbation</title>
@ -250,31 +250,31 @@ org_html_manager.setup(); // activate after the parameters are set
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org4e3f766">1. Summmary</a></li>
<li><a href="#org8e4d6b3">2. MP2</a>
<li><a href="#org41252b3">1. Summary</a></li>
<li><a href="#org049edc4">2. MP2</a>
<ul>
<li><a href="#orgafa22a1">2.1. Type</a></li>
<li><a href="#org0f17f3c">2.2. Creation</a></li>
<li><a href="#org6a18ed1">2.3. Access</a></li>
<li><a href="#orgb49bc14">2.4. Printers</a></li>
<li><a href="#orgd6b373f">2.5. Tests</a></li>
<li><a href="#org6bd6777">2.1. Type</a></li>
<li><a href="#orgb6b558e">2.2. Creation</a></li>
<li><a href="#orge04ea69">2.3. Access</a></li>
<li><a href="#org5c77b17">2.4. Printers</a></li>
<li><a href="#org676d466">2.5. Tests</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org4e3f766" class="outline-2">
<h2 id="org4e3f766"><span class="section-number-2">1</span> Summmary</h2>
<div id="outline-container-org41252b3" class="outline-2">
<h2 id="org41252b3"><span class="section-number-2">1</span> Summary</h2>
</div>
<div id="outline-container-org8e4d6b3" class="outline-2">
<h2 id="org8e4d6b3"><span class="section-number-2">2</span> MP2</h2>
<div id="outline-container-org049edc4" class="outline-2">
<h2 id="org049edc4"><span class="section-number-2">2</span> MP2</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-orgafa22a1" class="outline-3">
<h3 id="orgafa22a1"><span class="section-number-3">2.1</span> Type</h3>
<div id="outline-container-org6bd6777" class="outline-3">
<h3 id="org6bd6777"><span class="section-number-3">2.1</span> Type</h3>
<div class="outline-text-3" id="text-2-1">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span>
@ -283,8 +283,8 @@ org_html_manager.setup(); // activate after the parameters are set
</div>
</div>
<div id="outline-container-org0f17f3c" class="outline-3">
<h3 id="org0f17f3c"><span class="section-number-3">2.2</span> Creation</h3>
<div id="outline-container-orgb6b558e" class="outline-3">
<h3 id="orgb6b558e"><span class="section-number-3">2.2</span> Creation</h3>
<div class="outline-text-3" id="text-2-2">
<div class="org-src-container">
<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">frozen_core</span><span class="org-tuareg-font-lock-operator">:</span><span class="org-tuareg-font-lock-module">Mo.Frozen_core.</span>t <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Mo.Basis.</span>t <span class="org-tuareg-font-lock-operator">-&gt;</span> t
@ -307,7 +307,7 @@ org_html_manager.setup(); // activate after the parameters are set
</tbody>
</table>
<pre class="example" id="orgb30baf6">
<pre class="example" id="org758ab2e">
let mp2 =
Perturbation.Mp2.make ~frozen_core:(Mo.Frozen_core.(make Small nuclei)) mo_basis
;;
@ -316,8 +316,8 @@ val mp2 : Perturbation.Mp2.t = E(MP2)=-0.185523
</div>
</div>
<div id="outline-container-org6a18ed1" class="outline-3">
<h3 id="org6a18ed1"><span class="section-number-3">2.3</span> Access</h3>
<div id="outline-container-orge04ea69" class="outline-3">
<h3 id="orge04ea69"><span class="section-number-3">2.3</span> Access</h3>
<div class="outline-text-3" id="text-2-3">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">energy</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> float
@ -352,14 +352,14 @@ val mp2 : Perturbation.Mp2.t = E(MP2)=-0.185523
</tbody>
</table>
<pre class="example" id="org02ea73d">
<pre class="example" id="org2e825cc">
</pre>
</div>
</div>
<div id="outline-container-orgb49bc14" class="outline-3">
<h3 id="orgb49bc14"><span class="section-number-3">2.4</span> Printers</h3>
<div id="outline-container-org5c77b17" class="outline-3">
<h3 id="org5c77b17"><span class="section-number-3">2.4</span> Printers</h3>
<div class="outline-text-3" id="text-2-4">
<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">-&gt;</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> unit
@ -368,14 +368,14 @@ val mp2 : Perturbation.Mp2.t = E(MP2)=-0.185523
</div>
</div>
<div id="outline-container-orgd6b373f" class="outline-3">
<h3 id="orgd6b373f"><span class="section-number-3">2.5</span> Tests</h3>
<div id="outline-container-org676d466" class="outline-3">
<h3 id="org676d466"><span class="section-number-3">2.5</span> Tests</h3>
</div>
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: Anthony Scemama</p>
<p class="date">Created: 2021-01-27 Wed 23:44</p>
<p class="date">Created: 2021-10-19 Tue 16:20</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

10
docs/top.html
View File

@ -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>
<!-- 2021-02-03 Wed 10:47 -->
<!-- 2021-10-19 Tue 16:20 -->
<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>
@ -250,18 +250,18 @@ org_html_manager.setup(); // activate after the parameters are set
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgbfde666">1. Summmary</a></li>
<li><a href="#org5ece5ba">1. Summary</a></li>
</ul>
</div>
</div>
<div id="outline-container-orgbfde666" class="outline-2">
<h2 id="orgbfde666"><span class="section-number-2">1</span> Summmary</h2>
<div id="outline-container-org5ece5ba" class="outline-2">
<h2 id="org5ece5ba"><span class="section-number-2">1</span> Summary</h2>
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: Anthony Scemama</p>
<p class="date">Created: 2021-02-03 Wed 10:47</p>
<p class="date">Created: 2021-10-19 Tue 16:20</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

2
gaussian/README.org
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@ -1,7 +1,7 @@
#+TITLE: Gaussian
#+SETUPFILE: ../docs/theme.setup
* Summmary
* Summary
#+name: synopsis
#+begin_src ocaml :exports none :results value

2
gaussian_integrals/README.org
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@ -1,7 +1,7 @@
#+TITLE: Gaussian integrals
#+SETUPFILE: ../docs/theme.setup
* Summmary
* Summary
#+name: synopsis
#+begin_src ocaml :exports none :results value

2
linear_algebra/README.org
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@ -1,7 +1,7 @@
#+TITLE: Linear Algebra
#+SETUPFILE: ../docs/theme.setup
* Summmary
* Summary
#+name: synopsis
#+begin_src ocaml :exports none :results value

2
mo/README.org
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@ -1,7 +1,7 @@
#+TITLE: Molecular orbitals
#+SETUPFILE: ../docs/theme.setup
* Summmary
* Summary
#+name: synopsis
#+begin_src ocaml :exports none :results value

2
operators/README.org
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@ -1,7 +1,7 @@
#+TITLE: Operators
#+SETUPFILE: ../docs/theme.setup
* Summmary
* Summary
#+name: synopsis
#+begin_src ocaml :exports none :results value

2
particles/README.org
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@ -1,7 +1,7 @@
#+TITLE: Common
#+SETUPFILE: ../docs/theme.setup
* Summmary
* Summary
#+name: synopsis
#+begin_src ocaml :exports none :results value

2
perturbation/README.org
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@ -1,7 +1,7 @@
#+TITLE: Perturbation
#+SETUPFILE: ../docs/theme.setup
* Summmary
* Summary
#+name: synopsis
#+begin_src ocaml :exports none :results value

2
qcaml/README.org
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@ -1,7 +1,7 @@
#+TITLE: QCaml
#+SETUPFILE: ../docs/theme.setup
* Summmary
* Summary
#+name: synopsis
#+begin_src ocaml :exports none :results value

2
simulation/README.org
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@ -1,7 +1,7 @@
#+TITLE: Simulation
#+SETUPFILE: ../docs/theme.setup
* Summmary
* Summary
#+name: synopsis
#+begin_src ocaml :exports none :results value

2
top/README.org
View File

@ -1,7 +1,7 @@
#+TITLE: Top-level
#+SETUPFILE: ../docs/theme.setup
* Summmary
* Summary
#+name: synopsis
#+begin_src ocaml :exports none :results value