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Pretty printer for localization
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docs/mo.html
94
docs/mo.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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<!-- 2021-02-03 Wed 08:50 -->
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<!-- 2021-02-03 Wed 09:30 -->
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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>Molecular orbitals</title>
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@ -272,46 +272,46 @@ org_html_manager.setup(); // activate after the parameters are set
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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="#orgc090cb3">1. Summmary</a></li>
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<li><a href="#orgbe38590">2. Frozen core</a>
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<li><a href="#org0347fac">1. Summmary</a></li>
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<li><a href="#org3e52ccb">2. Frozen core</a>
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<ul>
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<li><a href="#org69d8070">2.1. Type</a></li>
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<li><a href="#orgcdbe863">2.2. Creation</a></li>
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<li><a href="#org8253c00">2.3. Access</a></li>
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<li><a href="#orgdec1d0a">2.4. Printers</a></li>
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<li><a href="#org314a379">2.1. Type</a></li>
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<li><a href="#org3f41ebf">2.2. Creation</a></li>
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<li><a href="#org30d9e55">2.3. Access</a></li>
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<li><a href="#orgbfbb067">2.4. Printers</a></li>
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</ul>
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</li>
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<li><a href="#org6309534">3. Orbital localization</a>
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<li><a href="#org71f8a17">3. Orbital localization</a>
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<ul>
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<li><a href="#orgf6eb1aa">3.1. Type</a></li>
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<li><a href="#org32bcf2c">3.2. Edmiston-Rudenberg</a></li>
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<li><a href="#orgced2d92">3.3. Boys</a></li>
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<li><a href="#org19e8774">3.4. Access</a></li>
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<li><a href="#orgb7676a6">3.5. Printers</a></li>
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<li><a href="#orgfbb396d">3.6. Tests</a></li>
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<li><a href="#orgd6cd073">3.1. Type</a></li>
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<li><a href="#org5abbc4c">3.2. Edmiston-Rudenberg</a></li>
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<li><a href="#org1360ab2">3.3. Boys</a></li>
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<li><a href="#org44850fb">3.4. Access</a></li>
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<li><a href="#orgb1a2fc0">3.5. Printers</a></li>
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<li><a href="#orgc751f7e">3.6. Tests</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 id="outline-container-orgc090cb3" class="outline-2">
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<h2 id="orgc090cb3"><span class="section-number-2">1</span> Summmary</h2>
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<div id="outline-container-org0347fac" class="outline-2">
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<h2 id="org0347fac"><span class="section-number-2">1</span> Summmary</h2>
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</div>
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<div id="outline-container-orgbe38590" class="outline-2">
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<h2 id="orgbe38590"><span class="section-number-2">2</span> Frozen core</h2>
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<div id="outline-container-org3e52ccb" class="outline-2">
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<h2 id="org3e52ccb"><span class="section-number-2">2</span> Frozen core</h2>
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<div class="outline-text-2" id="text-2">
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<p>
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Defines how the core electrons are frozen, for each atom.
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</p>
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</div>
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<div id="outline-container-org69d8070" class="outline-3">
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<h3 id="org69d8070"><span class="section-number-3">2.1</span> Type</h3>
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<div id="outline-container-org314a379" class="outline-3">
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<h3 id="org314a379"><span class="section-number-3">2.1</span> Type</h3>
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<div class="outline-text-3" id="text-2-1">
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<div class="org-src-container">
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<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>
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<pre class="src src-ocaml" id="org46bfdf8"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">kind</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">All_electron</span>
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<span class="org-tuareg-font-lock-operator">|</span> <span class="org-tuareg-font-lock-constructor">Small</span>
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<span class="org-tuareg-font-lock-operator">|</span> Large
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@ -325,8 +325,8 @@ Defines how the core electrons are frozen, for each atom.
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</div>
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</div>
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<div id="outline-container-orgcdbe863" class="outline-3">
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<h3 id="orgcdbe863"><span class="section-number-3">2.2</span> Creation</h3>
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<div id="outline-container-org3f41ebf" class="outline-3">
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<h3 id="org3f41ebf"><span class="section-number-3">2.2</span> Creation</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"><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">-></span> <span class="org-tuareg-font-lock-module">Particles.Nuclei.</span>t <span class="org-tuareg-font-lock-operator">-></span> t
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@ -362,7 +362,7 @@ Defines how the core electrons are frozen, for each atom.
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</tbody>
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</table>
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<pre class="example" id="org981a6c7">
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<pre class="example" id="org41e22ed">
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let f = Frozen_core.(make Small nuclei) ;;
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val f : Frozen_core.t = [|0; 2; 2; 0|]
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@ -372,8 +372,8 @@ val f : Frozen_core.t = [|0; 2; 2; 0|]
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</div>
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</div>
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<div id="outline-container-org8253c00" class="outline-3">
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<h3 id="org8253c00"><span class="section-number-3">2.3</span> Access</h3>
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<div id="outline-container-org30d9e55" class="outline-3">
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<h3 id="org30d9e55"><span class="section-number-3">2.3</span> Access</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">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">-></span> int
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@ -402,7 +402,7 @@ val f : Frozen_core.t = [|0; 2; 2; 0|]
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</tbody>
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</table>
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<pre class="example" id="org807dc16">
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<pre class="example" id="org64fff1a">
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Frozen_core.num_elec f ;;
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- : int = 4
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@ -412,8 +412,8 @@ Frozen_core.num_mos f ;;
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</div>
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</div>
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<div id="outline-container-orgdec1d0a" class="outline-3">
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<h3 id="orgdec1d0a"><span class="section-number-3">2.4</span> Printers</h3>
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<div id="outline-container-orgbfbb067" class="outline-3">
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<h3 id="orgbfbb067"><span class="section-number-3">2.4</span> Printers</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">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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@ -423,8 +423,8 @@ Frozen_core.num_mos f ;;
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</div>
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</div>
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<div id="outline-container-org6309534" class="outline-2">
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<h2 id="org6309534"><span class="section-number-2">3</span> Orbital localization</h2>
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<div id="outline-container-org71f8a17" class="outline-2">
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<h2 id="org71f8a17"><span class="section-number-2">3</span> Orbital localization</h2>
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<div class="outline-text-2" id="text-3">
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<p>
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Molecular orbital localization function.
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@ -440,11 +440,11 @@ Edmiston-Rudenberg:
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</div>
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<div id="outline-container-orgf6eb1aa" class="outline-3">
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<h3 id="orgf6eb1aa"><span class="section-number-3">3.1</span> Type</h3>
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<div id="outline-container-orgd6cd073" class="outline-3">
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<h3 id="orgd6cd073"><span class="section-number-3">3.1</span> Type</h3>
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<div class="outline-text-3" id="text-3-1">
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<div class="org-src-container">
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<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>
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<pre class="src src-ocaml" id="orgbd40984"><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">type</span> <span class="org-type">localization_kind</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">Edmiston</span>
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@ -464,16 +464,16 @@ Edmiston-Rudenberg:
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</div>
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</div>
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<div id="outline-container-org32bcf2c" class="outline-3">
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<h3 id="org32bcf2c"><span class="section-number-3">3.2</span> Edmiston-Rudenberg</h3>
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<div id="outline-container-org5abbc4c" class="outline-3">
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<h3 id="org5abbc4c"><span class="section-number-3">3.2</span> Edmiston-Rudenberg</h3>
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</div>
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<div id="outline-container-orgced2d92" class="outline-3">
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<h3 id="orgced2d92"><span class="section-number-3">3.3</span> Boys</h3>
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<div id="outline-container-org1360ab2" class="outline-3">
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<h3 id="org1360ab2"><span class="section-number-3">3.3</span> Boys</h3>
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</div>
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<div id="outline-container-org19e8774" class="outline-3">
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<h3 id="org19e8774"><span class="section-number-3">3.4</span> Access</h3>
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<div id="outline-container-org44850fb" class="outline-3">
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<h3 id="org44850fb"><span class="section-number-3">3.4</span> Access</h3>
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<div class="outline-text-3" id="text-3-4">
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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">kind</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-></span> localization_kind
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@ -522,26 +522,24 @@ Edmiston-Rudenberg:
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</div>
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</div>
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<div id="outline-container-orgb7676a6" class="outline-3">
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<h3 id="orgb7676a6"><span class="section-number-3">3.5</span> Printers</h3>
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<div id="outline-container-orgb1a2fc0" class="outline-3">
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<h3 id="orgb1a2fc0"><span class="section-number-3">3.5</span> Printers</h3>
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<div class="outline-text-3" id="text-3-5">
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<div class="org-src-container">
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<pre class="src src-ocaml"><span class="org-comment-delimiter">(*</span>
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<span class="org-comment"> val pp : Format.formatter -> t -> unit</span>
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<span class="org-comment"> </span><span class="org-comment-delimiter">*)</span>
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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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</pre>
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</div>
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</div>
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</div>
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<div id="outline-container-orgfbb396d" class="outline-3">
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<h3 id="orgfbb396d"><span class="section-number-3">3.6</span> Tests</h3>
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<div id="outline-container-orgc751f7e" class="outline-3">
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<h3 id="orgc751f7e"><span class="section-number-3">3.6</span> Tests</h3>
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</div>
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</div>
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</div>
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<div id="postamble" class="status">
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<p class="author">Author: Anthony Scemama</p>
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<p class="date">Created: 2021-02-03 Wed 08:50</p>
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<p class="date">Created: 2021-02-03 Wed 09:30</p>
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<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
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</div>
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</body>
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@ -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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<!-- 2021-02-03 Wed 08:50 -->
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<!-- 2021-02-03 Wed 09:30 -->
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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>Top-level</title>
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@ -250,18 +250,18 @@ org_html_manager.setup(); // activate after the parameters are set
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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="#orgb4e9044">1. Summmary</a></li>
|
||||
<li><a href="#org30505a3">1. Summmary</a></li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
|
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<div id="outline-container-orgb4e9044" class="outline-2">
|
||||
<h2 id="orgb4e9044"><span class="section-number-2">1</span> Summmary</h2>
|
||||
<div id="outline-container-org30505a3" class="outline-2">
|
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<h2 id="org30505a3"><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: 2021-02-03 Wed 08:50</p>
|
||||
<p class="date">Created: 2021-02-03 Wed 09:30</p>
|
||||
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
@ -15,6 +15,7 @@ type localization_data =
|
||||
kappa : (loc, loc) Matrix.t ;
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||||
scaling : float ;
|
||||
loc_value : float ;
|
||||
convergence : float ;
|
||||
iteration : int ;
|
||||
}
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||||
|
||||
@ -234,7 +235,7 @@ let ao_basis t = Simulation.ao_basis (simulation t)
|
||||
*)
|
||||
|
||||
|
||||
let make ~kind ?(max_iter=500) ?(convergence=1.e-8) mo_basis selected_mos =
|
||||
let make ~kind ?(max_iter=500) ?(convergence=1.e-6) mo_basis selected_mos =
|
||||
|
||||
let kappa_loc = kappa ~kind mo_basis in
|
||||
|
||||
@ -255,20 +256,27 @@ let make ~kind ?(max_iter=500) ?(convergence=1.e-8) mo_basis selected_mos =
|
||||
and scaling = 0.5
|
||||
in
|
||||
let kappa, loc_value = kappa_loc x in
|
||||
let convergence = abs_float (Matrix.amax kappa) in
|
||||
let kappa = Matrix.scale scaling kappa in
|
||||
let coefficients = next_coef kappa x in
|
||||
{ coefficients ; kappa ; scaling ; loc_value ; iteration }
|
||||
{ coefficients ; kappa ; scaling ; convergence ; loc_value ; iteration }
|
||||
in
|
||||
|
||||
let iteration data =
|
||||
let iteration = data.iteration + 1
|
||||
and scaling = data.scaling
|
||||
and x = data.coefficients
|
||||
in
|
||||
let kappa, loc_value = kappa_loc x in
|
||||
let convergence = abs_float (Matrix.amax kappa) in
|
||||
let scaling =
|
||||
if convergence <= data.convergence then
|
||||
min 1. (data.scaling *. 1.1)
|
||||
else
|
||||
data.scaling *. 0.75
|
||||
in
|
||||
let kappa = Matrix.scale scaling kappa in
|
||||
let coefficients = next_coef kappa x in
|
||||
{ coefficients ; kappa ; scaling ; loc_value ; iteration }
|
||||
{ coefficients ; kappa ; scaling ; convergence ; loc_value ; iteration }
|
||||
in
|
||||
|
||||
let array_data =
|
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@ -289,7 +297,7 @@ let make ~kind ?(max_iter=500) ?(convergence=1.e-8) mo_basis selected_mos =
|
||||
| Some data -> begin
|
||||
(* Check convergence *)
|
||||
let converged =
|
||||
abs_float data.loc_value < convergence
|
||||
data.convergence < convergence
|
||||
in
|
||||
if converged then
|
||||
None
|
||||
@ -327,5 +335,37 @@ let to_basis t =
|
||||
(* Access:2 ends here *)
|
||||
|
||||
(* [[file:~/QCaml/mo/localization.org::*Printers][Printers:2]] *)
|
||||
let linewidth = 60
|
||||
|
||||
let pp_iterations ppf t =
|
||||
let line = (String.make linewidth '-') in
|
||||
Format.fprintf ppf "@[%4s%s@]@." "" line;
|
||||
Format.fprintf ppf "@[%4s@[%5s@]@,@[%16s@]@,@[%16s@]@,@[%11s@]@]@."
|
||||
"" "#" "Localization " "Convergence" "Scaling";
|
||||
Format.fprintf ppf "@[%4s%s@]@." "" line;
|
||||
Array.iter (fun data ->
|
||||
let data = Lazy.force data in
|
||||
match data with
|
||||
| None -> ()
|
||||
| Some data ->
|
||||
let loc = data.loc_value in
|
||||
let conv = data.convergence in
|
||||
let scaling = data.scaling in
|
||||
let iteration = data.iteration in
|
||||
begin
|
||||
Format.fprintf ppf "@[%4s@[%5d@]@,@[%16.8f@]@,@[%16.4e@]@,@[%11.4f@]@]@." ""
|
||||
iteration loc conv scaling ;
|
||||
end
|
||||
) t.data;
|
||||
Format.fprintf ppf "@[%4s%s@]@." "" line
|
||||
|
||||
|
||||
let pp ppf t =
|
||||
Format.fprintf ppf "@.@[%s@]@." (String.make 70 '=');
|
||||
Format.fprintf ppf "@[%34s %-34s@]@." (match t.kind with
|
||||
| Boys -> "Boys"
|
||||
| Edmiston -> "Edmiston-Ruedenberg"
|
||||
) "MO Localization";
|
||||
Format.fprintf ppf "@[%s@]@.@." (String.make 70 '=');
|
||||
Format.fprintf ppf "@[%a@]@." pp_iterations t;
|
||||
(* Printers:2 ends here *)
|
||||
|
||||
@ -48,7 +48,5 @@ val to_basis : t -> Basis.t
|
||||
|
||||
|
||||
(* [[file:~/QCaml/mo/localization.org::*Printers][Printers:1]] *)
|
||||
(*
|
||||
val pp : Format.formatter -> t -> unit
|
||||
*)
|
||||
(* Printers:1 ends here *)
|
||||
|
||||
@ -50,6 +50,7 @@ type localization_data =
|
||||
kappa : (loc, loc) Matrix.t ;
|
||||
scaling : float ;
|
||||
loc_value : float ;
|
||||
convergence : float ;
|
||||
iteration : int ;
|
||||
}
|
||||
|
||||
@ -294,7 +295,7 @@ let ao_basis t = Simulation.ao_basis (simulation t)
|
||||
,*)
|
||||
|
||||
|
||||
let make ~kind ?(max_iter=500) ?(convergence=1.e-8) mo_basis selected_mos =
|
||||
let make ~kind ?(max_iter=500) ?(convergence=1.e-6) mo_basis selected_mos =
|
||||
|
||||
let kappa_loc = kappa ~kind mo_basis in
|
||||
|
||||
@ -315,20 +316,27 @@ let make ~kind ?(max_iter=500) ?(convergence=1.e-8) mo_basis selected_mos =
|
||||
and scaling = 0.5
|
||||
in
|
||||
let kappa, loc_value = kappa_loc x in
|
||||
let convergence = abs_float (Matrix.amax kappa) in
|
||||
let kappa = Matrix.scale scaling kappa in
|
||||
let coefficients = next_coef kappa x in
|
||||
{ coefficients ; kappa ; scaling ; loc_value ; iteration }
|
||||
{ coefficients ; kappa ; scaling ; convergence ; loc_value ; iteration }
|
||||
in
|
||||
|
||||
let iteration data =
|
||||
let iteration = data.iteration + 1
|
||||
and scaling = data.scaling
|
||||
and x = data.coefficients
|
||||
in
|
||||
let kappa, loc_value = kappa_loc x in
|
||||
let convergence = abs_float (Matrix.amax kappa) in
|
||||
let scaling =
|
||||
if convergence <= data.convergence then
|
||||
min 1. (data.scaling *. 1.1)
|
||||
else
|
||||
data.scaling *. 0.75
|
||||
in
|
||||
let kappa = Matrix.scale scaling kappa in
|
||||
let coefficients = next_coef kappa x in
|
||||
{ coefficients ; kappa ; scaling ; loc_value ; iteration }
|
||||
{ coefficients ; kappa ; scaling ; convergence ; loc_value ; iteration }
|
||||
in
|
||||
|
||||
let array_data =
|
||||
@ -349,7 +357,7 @@ let make ~kind ?(max_iter=500) ?(convergence=1.e-8) mo_basis selected_mos =
|
||||
| Some data -> begin
|
||||
(* Check convergence *)
|
||||
let converged =
|
||||
abs_float data.loc_value < convergence
|
||||
data.convergence < convergence
|
||||
in
|
||||
if converged then
|
||||
None
|
||||
@ -390,12 +398,43 @@ let to_basis t =
|
||||
** Printers
|
||||
|
||||
#+begin_src ocaml :tangle (eval mli)
|
||||
(*
|
||||
val pp : Format.formatter -> t -> unit
|
||||
*)
|
||||
#+end_src
|
||||
|
||||
#+begin_src ocaml :tangle (eval ml) :exports none
|
||||
let linewidth = 60
|
||||
|
||||
let pp_iterations ppf t =
|
||||
let line = (String.make linewidth '-') in
|
||||
Format.fprintf ppf "@[%4s%s@]@." "" line;
|
||||
Format.fprintf ppf "@[%4s@[%5s@]@,@[%16s@]@,@[%16s@]@,@[%11s@]@]@."
|
||||
"" "#" "Localization " "Convergence" "Scaling";
|
||||
Format.fprintf ppf "@[%4s%s@]@." "" line;
|
||||
Array.iter (fun data ->
|
||||
let data = Lazy.force data in
|
||||
match data with
|
||||
| None -> ()
|
||||
| Some data ->
|
||||
let loc = data.loc_value in
|
||||
let conv = data.convergence in
|
||||
let scaling = data.scaling in
|
||||
let iteration = data.iteration in
|
||||
begin
|
||||
Format.fprintf ppf "@[%4s@[%5d@]@,@[%16.8f@]@,@[%16.4e@]@,@[%11.4f@]@]@." ""
|
||||
iteration loc conv scaling ;
|
||||
end
|
||||
) t.data;
|
||||
Format.fprintf ppf "@[%4s%s@]@." "" line
|
||||
|
||||
|
||||
let pp ppf t =
|
||||
Format.fprintf ppf "@.@[%s@]@." (String.make 70 '=');
|
||||
Format.fprintf ppf "@[%34s %-34s@]@." (match t.kind with
|
||||
| Boys -> "Boys"
|
||||
| Edmiston -> "Edmiston-Ruedenberg"
|
||||
) "MO Localization";
|
||||
Format.fprintf ppf "@[%s@]@.@." (String.make 70 '=');
|
||||
Format.fprintf ppf "@[%a@]@." pp_iterations t;
|
||||
|
||||
#+end_src
|
||||
|
||||
|
||||
Loading…
Reference in New Issue
Block a user