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Fixed localization

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Anthony Scemama 2021-02-03 08:50:52 +01:00
parent 8e99b4a58c
commit 32c09e5d14
4 changed files with 52 additions and 52 deletions
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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>
<!-- 2021-02-01 Mon 16:35 -->
<!-- 2021-02-03 Wed 08:50 -->
<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="#org16b987d">1. Summmary</a></li>
<li><a href="#org0177256">2. Frozen core</a>
<li><a href="#orgc090cb3">1. Summmary</a></li>
<li><a href="#orgbe38590">2. Frozen core</a>
<ul>
<li><a href="#org6900aef">2.1. Type</a></li>
<li><a href="#org870a57f">2.2. Creation</a></li>
<li><a href="#org1166d5b">2.3. Access</a></li>
<li><a href="#orge10b2ae">2.4. Printers</a></li>
<li><a href="#org69d8070">2.1. Type</a></li>
<li><a href="#orgcdbe863">2.2. Creation</a></li>
<li><a href="#org8253c00">2.3. Access</a></li>
<li><a href="#orgdec1d0a">2.4. Printers</a></li>
</ul>
</li>
<li><a href="#org2fbb330">3. Orbital localization</a>
<li><a href="#org6309534">3. Orbital localization</a>
<ul>
<li><a href="#org03fdc29">3.1. Type</a></li>
<li><a href="#orgb4e9f2d">3.2. Edmiston-Rudenberg</a></li>
<li><a href="#org1896f76">3.3. Boys</a></li>
<li><a href="#org65fcd65">3.4. Access</a></li>
<li><a href="#org23e410d">3.5. Printers</a></li>
<li><a href="#orga62f968">3.6. Tests</a></li>
<li><a href="#orgf6eb1aa">3.1. Type</a></li>
<li><a href="#org32bcf2c">3.2. Edmiston-Rudenberg</a></li>
<li><a href="#orgced2d92">3.3. Boys</a></li>
<li><a href="#org19e8774">3.4. Access</a></li>
<li><a href="#orgb7676a6">3.5. Printers</a></li>
<li><a href="#orgfbb396d">3.6. Tests</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org16b987d" class="outline-2">
<h2 id="org16b987d"><span class="section-number-2">1</span> Summmary</h2>
<div id="outline-container-orgc090cb3" class="outline-2">
<h2 id="orgc090cb3"><span class="section-number-2">1</span> Summmary</h2>
</div>
<div id="outline-container-org0177256" class="outline-2">
<h2 id="org0177256"><span class="section-number-2">2</span> Frozen core</h2>
<div id="outline-container-orgbe38590" class="outline-2">
<h2 id="orgbe38590"><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-org6900aef" class="outline-3">
<h3 id="org6900aef"><span class="section-number-3">2.1</span> Type</h3>
<div id="outline-container-org69d8070" class="outline-3">
<h3 id="org69d8070"><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="org9eefac4"><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="org12d811a"><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-org870a57f" class="outline-3">
<h3 id="org870a57f"><span class="section-number-3">2.2</span> Creation</h3>
<div id="outline-container-orgcdbe863" class="outline-3">
<h3 id="orgcdbe863"><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="org983f6d9">
<pre class="example" id="org981a6c7">
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-org1166d5b" class="outline-3">
<h3 id="org1166d5b"><span class="section-number-3">2.3</span> Access</h3>
<div id="outline-container-org8253c00" class="outline-3">
<h3 id="org8253c00"><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="org0da2757">
<pre class="example" id="org807dc16">
Frozen_core.num_elec f ;;
- : int = 4
@ -412,8 +412,8 @@ Frozen_core.num_mos f ;;
</div>
</div>
<div id="outline-container-orge10b2ae" class="outline-3">
<h3 id="orge10b2ae"><span class="section-number-3">2.4</span> Printers</h3>
<div id="outline-container-orgdec1d0a" class="outline-3">
<h3 id="orgdec1d0a"><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-org2fbb330" class="outline-2">
<h2 id="org2fbb330"><span class="section-number-2">3</span> Orbital localization</h2>
<div id="outline-container-org6309534" class="outline-2">
<h2 id="org6309534"><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-org03fdc29" class="outline-3">
<h3 id="org03fdc29"><span class="section-number-3">3.1</span> Type</h3>
<div id="outline-container-orgf6eb1aa" class="outline-3">
<h3 id="orgf6eb1aa"><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="orgf4b2df1"><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="org60c20d2"><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-orgb4e9f2d" class="outline-3">
<h3 id="orgb4e9f2d"><span class="section-number-3">3.2</span> Edmiston-Rudenberg</h3>
<div id="outline-container-org32bcf2c" class="outline-3">
<h3 id="org32bcf2c"><span class="section-number-3">3.2</span> Edmiston-Rudenberg</h3>
</div>
<div id="outline-container-org1896f76" class="outline-3">
<h3 id="org1896f76"><span class="section-number-3">3.3</span> Boys</h3>
<div id="outline-container-orgced2d92" class="outline-3">
<h3 id="orgced2d92"><span class="section-number-3">3.3</span> Boys</h3>
</div>
<div id="outline-container-org65fcd65" class="outline-3">
<h3 id="org65fcd65"><span class="section-number-3">3.4</span> Access</h3>
<div id="outline-container-org19e8774" class="outline-3">
<h3 id="org19e8774"><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-org23e410d" class="outline-3">
<h3 id="org23e410d"><span class="section-number-3">3.5</span> Printers</h3>
<div id="outline-container-orgb7676a6" class="outline-3">
<h3 id="orgb7676a6"><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-comment-delimiter">(*</span>
@ -534,14 +534,14 @@ Edmiston-Rudenberg:
</div>
</div>
<div id="outline-container-orga62f968" class="outline-3">
<h3 id="orga62f968"><span class="section-number-3">3.6</span> Tests</h3>
<div id="outline-container-orgfbb396d" class="outline-3">
<h3 id="orgfbb396d"><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: 2021-02-01 Mon 16:35</p>
<p class="date">Created: 2021-02-03 Wed 08:50</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>
<!-- 2021-02-01 Mon 16:35 -->
<!-- 2021-02-03 Wed 08:50 -->
<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="#orgddd3ddd">1. Summmary</a></li>
<li><a href="#orgb4e9044">1. Summmary</a></li>
</ul>
</div>
</div>
<div id="outline-container-orgddd3ddd" class="outline-2">
<h2 id="orgddd3ddd"><span class="section-number-2">1</span> Summmary</h2>
<div id="outline-container-orgb4e9044" class="outline-2">
<h2 id="orgb4e9044"><span class="section-number-2">1</span> Summmary</h2>
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: Anthony Scemama</p>
<p class="date">Created: 2021-02-01 Mon 16:35</p>
<p class="date">Created: 2021-02-03 Wed 08:50</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

2
mo/lib/localization.ml
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@ -321,7 +321,7 @@ let to_basis t =
Matrix.to_col_vecs data.coefficients
in
selected_mos t
|> List.iteri (fun i j -> mo_coef_array.(j) <- new_mos.(i)) ;
|> List.iteri (fun i j -> mo_coef_array.(j-1) <- new_mos.(i)) ;
let mo_coef = Matrix.of_col_vecs mo_coef_array in
Basis.make ~simulation ~mo_type:(Localized "Boys") ~mo_occupation ~mo_coef ()
(* Access:2 ends here *)

2
mo/localization.org
View File

@ -381,7 +381,7 @@ let to_basis t =
Matrix.to_col_vecs data.coefficients
in
selected_mos t
|> List.iteri (fun i j -> mo_coef_array.(j) <- new_mos.(i)) ;
|> List.iteri (fun i j -> mo_coef_array.(j-1) <- new_mos.(i)) ;
let mo_coef = Matrix.of_col_vecs mo_coef_array in
Basis.make ~simulation ~mo_type:(Localized "Boys") ~mo_occupation ~mo_coef ()