mirror of https://gitlab.com/scemama/QCaml.git
Moving all MOs is not optimal
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docs/mo.html
90
docs/mo.html
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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 09:30 -->
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<!-- 2021-02-03 Wed 10:47 -->
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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="#org0347fac">1. Summmary</a></li>
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<li><a href="#org3e52ccb">2. Frozen core</a>
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<li><a href="#org16f6c6b">1. Summmary</a></li>
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<li><a href="#orgebbcfe0">2. Frozen core</a>
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<ul>
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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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<li><a href="#org61f3b2e">2.1. Type</a></li>
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<li><a href="#orgfff2d7e">2.2. Creation</a></li>
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<li><a href="#org2519af7">2.3. Access</a></li>
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<li><a href="#orga5fe616">2.4. Printers</a></li>
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</ul>
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</li>
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<li><a href="#org71f8a17">3. Orbital localization</a>
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<li><a href="#org03637a8">3. Orbital localization</a>
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<ul>
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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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<li><a href="#orge723841">3.1. Type</a></li>
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<li><a href="#org6933918">3.2. Edmiston-Rudenberg</a></li>
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<li><a href="#org44c9408">3.3. Boys</a></li>
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<li><a href="#org64dada8">3.4. Access</a></li>
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<li><a href="#org5b86753">3.5. Printers</a></li>
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<li><a href="#orgcfa3655">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-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 id="outline-container-org16f6c6b" class="outline-2">
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<h2 id="org16f6c6b"><span class="section-number-2">1</span> Summmary</h2>
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</div>
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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 id="outline-container-orgebbcfe0" class="outline-2">
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<h2 id="orgebbcfe0"><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-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 id="outline-container-org61f3b2e" class="outline-3">
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<h3 id="org61f3b2e"><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="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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<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>
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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-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 id="outline-container-orgfff2d7e" class="outline-3">
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<h3 id="orgfff2d7e"><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="org41e22ed">
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<pre class="example" id="org863654b">
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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-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 id="outline-container-org2519af7" class="outline-3">
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<h3 id="org2519af7"><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="org64fff1a">
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<pre class="example" id="org517ff86">
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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-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 id="outline-container-orga5fe616" class="outline-3">
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<h3 id="orga5fe616"><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-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 id="outline-container-org03637a8" class="outline-2">
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<h2 id="org03637a8"><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-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 id="outline-container-orge723841" class="outline-3">
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<h3 id="orge723841"><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="orgbd40984"><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="org1b6afe0"><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-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 id="outline-container-org6933918" class="outline-3">
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<h3 id="org6933918"><span class="section-number-3">3.2</span> Edmiston-Rudenberg</h3>
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</div>
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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 id="outline-container-org44c9408" class="outline-3">
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<h3 id="org44c9408"><span class="section-number-3">3.3</span> Boys</h3>
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</div>
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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 id="outline-container-org64dada8" class="outline-3">
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<h3 id="org64dada8"><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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@ -522,8 +522,8 @@ Edmiston-Rudenberg:
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</div>
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</div>
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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 id="outline-container-org5b86753" class="outline-3">
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<h3 id="org5b86753"><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-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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@ -532,14 +532,14 @@ Edmiston-Rudenberg:
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</div>
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</div>
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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 id="outline-container-orgcfa3655" class="outline-3">
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<h3 id="orgcfa3655"><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 09:30</p>
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<p class="date">Created: 2021-02-03 Wed 10:47</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 09:30 -->
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<!-- 2021-02-03 Wed 10:47 -->
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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="#org30505a3">1. Summmary</a></li>
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<li><a href="#orgbfde666">1. Summmary</a></li>
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</ul>
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</div>
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</div>
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<div id="outline-container-org30505a3" class="outline-2">
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<h2 id="org30505a3"><span class="section-number-2">1</span> Summmary</h2>
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<div id="outline-container-orgbfde666" class="outline-2">
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<h2 id="orgbfde666"><span class="section-number-2">1</span> Summmary</h2>
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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 09:30</p>
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<p class="date">Created: 2021-02-03 Wed 10:47</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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@ -2,6 +2,7 @@
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(names
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ex_integrals
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ex_hartree_fock
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ex_localization
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)
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(libraries qcaml))
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@ -0,0 +1,170 @@
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(* ./run_Localisation.native -b basis -x xyz -c charge -o name.mos -i EZFIOdirectory > name.out *)
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(*
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#.mos contains the localised orbitales
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#.out contains the localization convergence and the analysis of the spatial extent of the orbitales
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*)
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open Qcaml
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module Command_line = Common.Command_line
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module Util = Common.Util
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module Range = Common.Range
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module Electrons = Particles.Electrons
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open Linear_algebra
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let read_qp_mo dirname =
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let ic = Unix.open_process_in ("zcat "^dirname^"/mo_basis/mo_coef.gz") in
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let check = String.trim (input_line ic) in
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assert (check = "2");
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let int_list =
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input_line ic
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|> String.split_on_char ' '
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|> List.filter (fun x -> x <> "")
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|> List.map int_of_string
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in
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let n_ao, n_mo =
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match int_list with
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| [ x ; y ] -> x, y
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| _ -> assert false
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in
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let result =
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Matrix.init_cols n_ao n_mo (fun _ _ ->
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let s = input_line ic in
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Scanf.sscanf s " %f " (fun x -> x)
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)
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in
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let exit_code = Unix.close_process_in ic in
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assert (exit_code = Unix.WEXITED 0);
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result
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|
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let () =
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let open Command_line in
|
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begin
|
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set_header_doc (Sys.argv.(0) ^ " - QCaml command");
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set_description_doc "Localizes MOs";
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set_specs
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[ { short='b' ; long="basis" ; opt=Mandatory;
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arg=With_arg "<string>";
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doc="Name of the file containing the basis set"; } ;
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||||
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{ short='x' ; long="xyz" ; opt=Mandatory;
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arg=With_arg "<string>";
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doc="Name of the file containing the nuclear coordinates in xyz format"; } ;
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||||
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{ short='m' ; long="multiplicity" ; opt=Optional;
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arg=With_arg "<int>";
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doc="Spin multiplicity (2S+1). Default is singlet"; } ;
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{ short='c' ; long="charge" ; opt=Optional;
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arg=With_arg "<int>";
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doc="Total charge of the molecule. Default is 0"; } ;
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{ short='o' ; long="output" ; opt=Mandatory;
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arg=With_arg "<string>";
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doc="Name of the file containing the localized MOs"; } ;
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{ short='i' ; long="import" ; opt=Optional;
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arg=With_arg "<string>";
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doc="Name of the EZFIO directory containing MOs"; } ;
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{ short='r' ; long="range" ; opt=Mandatory;
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arg=With_arg "<range>";
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doc="Range of orbitals to include in localization"; } ;
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||||
]
|
||||
end;
|
||||
|
||||
|
||||
|
||||
(* II : Hartree-Fock *)
|
||||
|
||||
(* 1. Def pour HF *)
|
||||
|
||||
let basis_file = Util.of_some @@ Command_line.get "basis" in
|
||||
let nuclei_file = Util.of_some @@ Command_line.get "xyz" in
|
||||
|
||||
let charge =
|
||||
match Command_line.get "charge" with
|
||||
| Some x -> ( if x.[0] = 'm' then
|
||||
~- (int_of_string (String.sub x 1 (String.length x - 1)))
|
||||
else
|
||||
int_of_string x )
|
||||
| None -> 0
|
||||
in
|
||||
|
||||
let multiplicity =
|
||||
match Command_line.get "multiplicity" with
|
||||
| Some x -> int_of_string x
|
||||
| None -> 1
|
||||
in
|
||||
|
||||
let range =
|
||||
Command_line.get "range"
|
||||
|> Util.of_some
|
||||
|> Range.of_string
|
||||
|> Range.to_int_list
|
||||
in
|
||||
|
||||
let ezfio_file = Command_line.get "import" in
|
||||
|
||||
let output_filename = Util.of_some @@ Command_line.get "output" in
|
||||
(* Interpretation:1 ends here *)
|
||||
|
||||
(* [[file:~/QCaml/examples/ex_hartree_fock.org::*Computation][Computation:1]] *)
|
||||
let nuclei =
|
||||
Qcaml.Particles.Nuclei.of_xyz_file nuclei_file
|
||||
in
|
||||
(* Computation:1 ends here *)
|
||||
|
||||
(* [[file:~/QCaml/examples/ex_hartree_fock.org::*Computation][Computation:2]] *)
|
||||
let ao_basis =
|
||||
Qcaml.Ao.Basis.of_nuclei_and_basis_filename ~nuclei basis_file
|
||||
in
|
||||
(* Computation:2 ends here *)
|
||||
|
||||
|
||||
let simulation =
|
||||
Simulation.make ~charge ~multiplicity ~nuclei ao_basis
|
||||
in
|
||||
|
||||
(* 2. Calcul de Hartree-Fock*)
|
||||
let mo_basis =
|
||||
match ezfio_file with
|
||||
| Some ezfio_file ->
|
||||
let mo_coef = read_qp_mo ezfio_file in
|
||||
let mo_type = Mo.Basis.Localized "Boys" in
|
||||
let elec = Simulation.electrons simulation in
|
||||
let n_mo = Matrix.dim2 mo_coef in
|
||||
let mo_occupation = Vector.init n_mo (fun i ->
|
||||
if i <= Electrons.n_beta elec then 2.
|
||||
else if i <= Electrons.n_alfa elec then 1.
|
||||
else 0.) in
|
||||
Mo.Basis.make ~simulation ~mo_type ~mo_occupation ~mo_coef ()
|
||||
| None -> Mo.Hartree_fock.make simulation
|
||||
|> Mo.Basis.of_hartree_fock
|
||||
in
|
||||
|
||||
|
||||
let localization =
|
||||
Mo.Localization.make ~kind:Mo.Localization.Boys mo_basis range
|
||||
in
|
||||
|
||||
Format.printf "@[%a@]" (Mo.Localization.pp) localization;
|
||||
|
||||
let local_mo_basis =
|
||||
Mo.Localization.to_basis localization
|
||||
in
|
||||
|
||||
let local_mos =
|
||||
Mo.Basis.mo_coef local_mo_basis
|
||||
in
|
||||
|
||||
let oc = open_out output_filename in
|
||||
Printf.fprintf oc "[\n";
|
||||
Matrix.as_vec local_mos
|
||||
|> Vector.iter (fun x -> Printf.fprintf oc "%20.15e,\n" x);
|
||||
Printf.fprintf oc "]\n";
|
||||
close_out oc
|
||||
|
|
@ -253,7 +253,7 @@ let make ~kind ?(max_iter=500) ?(convergence=1.e-6) mo_basis selected_mos =
|
|||
|
||||
let data_initial =
|
||||
let iteration = 0
|
||||
and scaling = 0.5
|
||||
and scaling = 0.1
|
||||
in
|
||||
let kappa, loc_value = kappa_loc x in
|
||||
let convergence = abs_float (Matrix.amax kappa) in
|
||||
|
|
@ -263,20 +263,24 @@ let make ~kind ?(max_iter=500) ?(convergence=1.e-6) mo_basis selected_mos =
|
|||
in
|
||||
|
||||
let iteration data =
|
||||
let iteration = data.iteration + 1
|
||||
and x = data.coefficients
|
||||
let iteration = data.iteration+1 in
|
||||
let new_kappa, new_loc_value = kappa_loc data.coefficients in
|
||||
let new_convergence = abs_float (Matrix.amax new_kappa) in
|
||||
let accept =
|
||||
new_loc_value >= data.loc_value*.0.98
|
||||
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 ; convergence ; loc_value ; iteration }
|
||||
if accept then
|
||||
let coefficients = next_coef new_kappa data.coefficients in
|
||||
let scaling = min 1. (data.scaling *. 1.1) in
|
||||
let kappa = Matrix.scale scaling new_kappa in
|
||||
let convergence = new_convergence in
|
||||
let loc_value = new_loc_value in
|
||||
{ coefficients ; kappa ; scaling ; convergence ; loc_value ; iteration }
|
||||
else
|
||||
let scaling =
|
||||
data.scaling *. 0.5
|
||||
in
|
||||
{ data with scaling ; iteration }
|
||||
in
|
||||
|
||||
let array_data =
|
||||
|
|
|
|||
|
|
@ -313,7 +313,7 @@ let make ~kind ?(max_iter=500) ?(convergence=1.e-6) mo_basis selected_mos =
|
|||
|
||||
let data_initial =
|
||||
let iteration = 0
|
||||
and scaling = 0.5
|
||||
and scaling = 0.1
|
||||
in
|
||||
let kappa, loc_value = kappa_loc x in
|
||||
let convergence = abs_float (Matrix.amax kappa) in
|
||||
|
|
@ -323,20 +323,24 @@ let make ~kind ?(max_iter=500) ?(convergence=1.e-6) mo_basis selected_mos =
|
|||
in
|
||||
|
||||
let iteration data =
|
||||
let iteration = data.iteration + 1
|
||||
and x = data.coefficients
|
||||
let iteration = data.iteration+1 in
|
||||
let new_kappa, new_loc_value = kappa_loc data.coefficients in
|
||||
let new_convergence = abs_float (Matrix.amax new_kappa) in
|
||||
let accept =
|
||||
new_loc_value >= data.loc_value*.0.98
|
||||
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 ; convergence ; loc_value ; iteration }
|
||||
if accept then
|
||||
let coefficients = next_coef new_kappa data.coefficients in
|
||||
let scaling = min 1. (data.scaling *. 1.1) in
|
||||
let kappa = Matrix.scale scaling new_kappa in
|
||||
let convergence = new_convergence in
|
||||
let loc_value = new_loc_value in
|
||||
{ coefficients ; kappa ; scaling ; convergence ; loc_value ; iteration }
|
||||
else
|
||||
let scaling =
|
||||
data.scaling *. 0.5
|
||||
in
|
||||
{ data with scaling ; iteration }
|
||||
in
|
||||
|
||||
let array_data =
|
||||
|
|
|
|||
Loading…
Reference in New Issue