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Added HTML documentation

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Anthony Scemama 2021-01-01 17:05:25 +01:00
parent 73a5cf6ca2
commit 08bd5303d9
30 changed files with 916 additions and 420 deletions
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3
.gitmodules vendored Normal file
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@ -0,0 +1,3 @@
[submodule "docs/org-html-themes"]
path = docs/org-html-themes
url = https://github.com/fniessen/org-html-themes.git

4
Makefile
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@ -5,7 +5,7 @@ DOCS=$(patsubst %, docs/%.html, $(DIRS))
.PHONY: default build install uninstall test clean
default: tangle build doc
default: build
docs/%.html: %/README.org
@ -14,7 +14,7 @@ docs/%.html: %/README.org
doc: $(DOCS)
build:
build: doc
dune build
test:

2
ao/README.org
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@ -1,5 +1,5 @@
#+TITLE: Atomic Orbitals
#+SETUPFILE: https://fniessen.github.io/org-html-themes/org/theme-readtheorg.setup
#+SETUPFILE: ../docs/org-html-themes/org/theme-readtheorg.setup
#+name: synopsis
#+begin_src ocaml :export output raw

5
bin/build_doc.sh
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@ -22,8 +22,7 @@ done
CONFIG="--load docs/htmlize.el --load docs/config.el"
emacs --batch $CONFIG docs/${DIR}.org -f org-html-export-to-html
rm docs/${DIR}.org
emacs --debug-init --batch $CONFIG docs/${DIR}.org -f org-html-export-to-html \
&& rm docs/${DIR}.org

2
common/README.org
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@ -1,5 +1,5 @@
#+TITLE: Common
#+SETUPFILE: https://fniessen.github.io/org-html-themes/org/theme-readtheorg.setup
#+SETUPFILE: ../docs/org-html-themes/org/theme-readtheorg.setup
#+name: synopsis

6
docs/ao.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>
<!-- 2021-01-01 Fri 16:38 -->
<!-- 2021-01-01 Fri 17:04 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Atomic Orbitals</title>
@ -226,13 +226,13 @@
<div id="content">
<h1 class="title">Atomic Orbitals</h1>
<div class="org-src-container">
<pre class="src src-ocaml" id="orgb54ee80"><span class="org-string">"Atomic basis set"</span>
<pre class="src src-ocaml" id="org4d387db"><span class="org-string">"Atomic basis set"</span>
</pre>
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: Anthony Scemama</p>
<p class="date">Created: 2021-01-01 Fri 16:38</p>
<p class="date">Created: 2021-01-01 Fri 17:04</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

462
docs/common.html
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File diff suppressed because it is too large Load Diff

16
docs/config.el
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@ -6,6 +6,22 @@
(require 'font-lock)
(require 'subr-x) ;; for `when-let'
(org-babel-do-load-languages
'org-babel-load-languages
'(
(emacs-lisp . t)
(shell . t)
(python . t)
(C . t)
(ocaml . t)
(gnuplot . t)
(latex . t)
(ditaa . t)
(dot . t)
(org . t)
(makefile . t)
))
(unless (boundp 'maximal-integer)
(defconst maximal-integer (lsh -1 -1)
"Maximal integer value representable natively in emacs lisp."))

6
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>
<!-- 2021-01-01 Fri 16:38 -->
<!-- 2021-01-01 Fri 17:04 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Gaussian</title>
@ -226,13 +226,13 @@
<div id="content">
<h1 class="title">Gaussian</h1>
<div class="org-src-container">
<pre class="src src-ocaml" id="org5fcfd15"><span class="org-string">"Gaussian basis sets"</span>
<pre class="src src-ocaml" id="org48e0290"><span class="org-string">"Gaussian basis sets"</span>
</pre>
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: Anthony Scemama</p>
<p class="date">Created: 2021-01-01 Fri 16:38</p>
<p class="date">Created: 2021-01-01 Fri 17:04</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

6
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>
<!-- 2021-01-01 Fri 16:38 -->
<!-- 2021-01-01 Fri 17:04 -->
<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>
@ -226,13 +226,13 @@
<div id="content">
<h1 class="title">Gaussian integrals</h1>
<div class="org-src-container">
<pre class="src src-ocaml" id="orgf36fc27"><span class="org-string">"Integrals on the Gaussian basis sets"</span>
<pre class="src src-ocaml" id="orgc76074e"><span class="org-string">"Integrals on the Gaussian basis sets"</span>
</pre>
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: Anthony Scemama</p>
<p class="date">Created: 2021-01-01 Fri 16:38</p>
<p class="date">Created: 2021-01-01 Fri 17:04</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

6
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>
<!-- 2021-01-01 Fri 16:38 -->
<!-- 2021-01-01 Fri 17:04 -->
<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>
@ -226,13 +226,13 @@
<div id="content">
<h1 class="title">Linear Algebra</h1>
<div class="org-src-container">
<pre class="src src-ocaml" id="org6e8c657"><span class="org-string">"Linear algebra utilities of QCaml libraries."</span>
<pre class="src src-ocaml" id="org0c846f4"><span class="org-string">"Linear algebra utilities of QCaml libraries."</span>
</pre>
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: Anthony Scemama</p>
<p class="date">Created: 2021-01-01 Fri 16:38</p>
<p class="date">Created: 2021-01-01 Fri 17:04</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

42
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>
<!-- 2021-01-01 Fri 16:38 -->
<!-- 2021-01-01 Fri 17:04 -->
<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>
@ -229,36 +229,36 @@
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org9d1c0a9">1. Frozen core</a>
<li><a href="#org19d2f10">1. Frozen core</a>
<ul>
<li><a href="#org1c7c95a">1.1. Type</a></li>
<li><a href="#orgb2586e7">1.2. Creation</a></li>
<li><a href="#org482997a">1.3. Access</a></li>
<li><a href="#orga5d7816">1.4. Printers</a></li>
<li><a href="#orgb226c61">1.1. Type</a></li>
<li><a href="#org9e3a631">1.2. Creation</a></li>
<li><a href="#orgd1f52ba">1.3. Access</a></li>
<li><a href="#org5cc9b8f">1.4. Printers</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div class="org-src-container">
<pre class="src src-ocaml" id="org7d44fe6"><span class="org-string">"Molecular orbitals"</span>
<pre class="src src-ocaml" id="orgda95157"><span class="org-string">"Molecular orbitals"</span>
</pre>
</div>
<div id="outline-container-org9d1c0a9" class="outline-2">
<h2 id="org9d1c0a9"><span class="section-number-2">1</span> Frozen core</h2>
<div id="outline-container-org19d2f10" class="outline-2">
<h2 id="org19d2f10"><span class="section-number-2">1</span> Frozen core</h2>
<div class="outline-text-2" id="text-1">
<p>
Defines how the core electrons are frozen, for each atom.
</p>
</div>
<div id="outline-container-org1c7c95a" class="outline-3">
<h3 id="org1c7c95a"><span class="section-number-3">1.1</span> Type</h3>
<div id="outline-container-orgb226c61" class="outline-3">
<h3 id="orgb226c61"><span class="section-number-3">1.1</span> Type</h3>
<div class="outline-text-3" id="text-1-1">
<div class="org-src-container">
<pre class="src src-ocaml" id="org2ed636d"><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="org12f94d0"><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
@ -272,8 +272,8 @@ Defines how the core electrons are frozen, for each atom.
</div>
</div>
<div id="outline-container-orgb2586e7" class="outline-3">
<h3 id="orgb2586e7"><span class="section-number-3">1.2</span> Creation</h3>
<div id="outline-container-org9e3a631" class="outline-3">
<h3 id="org9e3a631"><span class="section-number-3">1.2</span> Creation</h3>
<div class="outline-text-3" id="text-1-2">
<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
@ -309,7 +309,7 @@ Defines how the core electrons are frozen, for each atom.
</tbody>
</table>
<pre class="example" id="org7332159">
<pre class="example" id="org8cde3b0">
let f = Frozen_core.(make Small nuclei) ;;
val f : Frozen_core.t = [|0; 2; 2; 0|]
@ -319,8 +319,8 @@ val f : Frozen_core.t = [|0; 2; 2; 0|]
</div>
</div>
<div id="outline-container-org482997a" class="outline-3">
<h3 id="org482997a"><span class="section-number-3">1.3</span> Access</h3>
<div id="outline-container-orgd1f52ba" class="outline-3">
<h3 id="orgd1f52ba"><span class="section-number-3">1.3</span> Access</h3>
<div class="outline-text-3" id="text-1-3">
<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
@ -349,7 +349,7 @@ val f : Frozen_core.t = [|0; 2; 2; 0|]
</tbody>
</table>
<pre class="example" id="org1d3352f">
<pre class="example" id="org7fbf5c4">
Frozen_core.num_elec f ;;
- : int = 4
@ -359,8 +359,8 @@ Frozen_core.num_mos f ;;
</div>
</div>
<div id="outline-container-orga5d7816" class="outline-3">
<h3 id="orga5d7816"><span class="section-number-3">1.4</span> Printers</h3>
<div id="outline-container-org5cc9b8f" class="outline-3">
<h3 id="org5cc9b8f"><span class="section-number-3">1.4</span> Printers</h3>
<div class="outline-text-3" id="text-1-4">
<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
@ -372,7 +372,7 @@ Frozen_core.num_mos f ;;
</div>
<div id="postamble" class="status">
<p class="author">Author: Anthony Scemama</p>
<p class="date">Created: 2021-01-01 Fri 16:38</p>
<p class="date">Created: 2021-01-01 Fri 17:04</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

6
docs/operators.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>
<!-- 2021-01-01 Fri 16:38 -->
<!-- 2021-01-01 Fri 17:04 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Operators</title>
@ -226,13 +226,13 @@
<div id="content">
<h1 class="title">Operators</h1>
<div class="org-src-container">
<pre class="src src-ocaml" id="org0a9530e"><span class="org-string">"Parameteried operators, such as F12 and range-separation"</span>
<pre class="src src-ocaml" id="orge2a70f3"><span class="org-string">"Parameteried operators, such as F12 and range-separation"</span>
</pre>
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: Anthony Scemama</p>
<p class="date">Created: 2021-01-01 Fri 16:38</p>
<p class="date">Created: 2021-01-01 Fri 17:04</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

1
docs/org-html-themes Submodule

@ -0,0 +1 @@
Subproject commit 885ddd8451a3b1952628a52c4eeebf0a3d86d33a

170
docs/particles.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>
<!-- 2021-01-01 Fri 16:37 -->
<!-- 2021-01-01 Fri 17:04 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Common</title>
@ -251,75 +251,75 @@
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgf947286">1. Electrons</a>
<li><a href="#orgd29e276">1. Electrons</a>
<ul>
<li><a href="#orgb7eb1f5">1.1. Type</a></li>
<li><a href="#org2109b26">1.2. Creation</a></li>
<li><a href="#org2a36970">1.3. Access</a></li>
<li><a href="#org5e47047">1.4. Printers</a></li>
<li><a href="#orgc347c9f">1.5. Tests</a></li>
<li><a href="#org797cc3a">1.1. Type</a></li>
<li><a href="#org2bed657">1.2. Creation</a></li>
<li><a href="#org2672eeb">1.3. Access</a></li>
<li><a href="#org8f61c62">1.4. Printers</a></li>
<li><a href="#org0d76e84">1.5. Tests</a></li>
</ul>
</li>
<li><a href="#org25852ad">2. Element</a>
<li><a href="#org904d88b">2. Element</a>
<ul>
<li><a href="#org038a472">2.1. Type</a></li>
<li><a href="#orgc0d1c8c">2.2. Conversion</a></li>
<li><a href="#orgf48d5b6">2.3. Database information</a></li>
<li><a href="#org4e97465">2.4. Printers</a></li>
<li><a href="#org0f44138">2.1. Type</a></li>
<li><a href="#org3260b21">2.2. Conversion</a></li>
<li><a href="#orgecbb559">2.3. Database information</a></li>
<li><a href="#org4204ce9">2.4. Printers</a></li>
</ul>
</li>
<li><a href="#org4c5689f">3. Atomic mass</a></li>
<li><a href="#org6bd3bbb">4. Nuclei</a>
<li><a href="#orgc37ce9d">3. Atomic mass</a></li>
<li><a href="#org485ac9f">4. Nuclei</a>
<ul>
<li><a href="#org91c1c84">4.1. Type</a></li>
<li><a href="#org0e06d85">4.2. xyz file lexer/parser</a>
<li><a href="#org02f7836">4.1. Type</a></li>
<li><a href="#orgfdafdd0">4.2. xyz file lexer/parser</a>
<ul>
<li><a href="#orgd2a815e">4.2.1. Lexer</a></li>
<li><a href="#orga0e9364">4.2.2. Parser</a></li>
<li><a href="#orgeddfd39">4.2.1. Lexer</a></li>
<li><a href="#orgb1e9400">4.2.2. Parser</a></li>
</ul>
</li>
<li><a href="#org67c4576">4.3. Conversion</a></li>
<li><a href="#org31c8415">4.4. <span class="todo TODO">TODO</span> Query</a></li>
<li><a href="#orga01f8b6">4.5. Printers</a></li>
<li><a href="#orgf2e9bac">4.6. Tests</a></li>
<li><a href="#org19995b8">4.3. Conversion</a></li>
<li><a href="#org57fb733">4.4. <span class="todo TODO">TODO</span> Query</a></li>
<li><a href="#org87456a6">4.5. Printers</a></li>
<li><a href="#org60012a5">4.6. Tests</a></li>
</ul>
</li>
<li><a href="#org3573ea4">5. Z-matrix</a>
<li><a href="#org72daeec">5. Z-matrix</a>
<ul>
<li><a href="#org7593a50">5.1. Type</a></li>
<li><a href="#orgf0cdae8">5.2. Conversion</a></li>
<li><a href="#org08080f5">5.3. Printers</a></li>
<li><a href="#org0859680">5.1. Type</a></li>
<li><a href="#org9ab67d9">5.2. Conversion</a></li>
<li><a href="#org442f12d">5.3. Printers</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div class="org-src-container">
<pre class="src src-ocaml" id="org62b2bfe"><span class="org-string">"Information relative to particles (electrons and nuclei)."</span>
<pre class="src src-ocaml" id="orgb5cf5bb"><span class="org-string">"Information relative to particles (electrons and nuclei)."</span>
</pre>
</div>
<div id="outline-container-orgf947286" class="outline-2">
<h2 id="orgf947286"><span class="section-number-2">1</span> Electrons</h2>
<div id="outline-container-orgd29e276" class="outline-2">
<h2 id="orgd29e276"><span class="section-number-2">1</span> Electrons</h2>
<div class="outline-text-2" id="text-1">
<p>
Data structure which contains the number of &alpha; and &beta; electrons.
</p>
</div>
<div id="outline-container-orgb7eb1f5" class="outline-3">
<h3 id="orgb7eb1f5"><span class="section-number-3">1.1</span> Type</h3>
<div id="outline-container-org797cc3a" class="outline-3">
<h3 id="org797cc3a"><span class="section-number-3">1.1</span> Type</h3>
<div class="outline-text-3" id="text-1-1">
<div class="org-src-container">
<pre class="src src-ocaml" id="orge3b79fc"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span>
<pre class="src src-ocaml" id="org86ddc6e"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span>
</pre>
</div>
</div>
</div>
<div id="outline-container-org2109b26" class="outline-3">
<h3 id="org2109b26"><span class="section-number-3">1.2</span> Creation</h3>
<div id="outline-container-org2bed657" class="outline-3">
<h3 id="org2bed657"><span class="section-number-3">1.2</span> Creation</h3>
<div class="outline-text-3" id="text-1-2">
<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>
@ -358,8 +358,8 @@ Data structure which contains the number of &alpha; and &beta; electrons.
</div>
</div>
<div id="outline-container-org2a36970" class="outline-3">
<h3 id="org2a36970"><span class="section-number-3">1.3</span> Access</h3>
<div id="outline-container-org2672eeb" class="outline-3">
<h3 id="org2672eeb"><span class="section-number-3">1.3</span> Access</h3>
<div class="outline-text-3" id="text-1-3">
<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
@ -408,8 +408,8 @@ Data structure which contains the number of &alpha; and &beta; electrons.
</div>
</div>
<div id="outline-container-org5e47047" class="outline-3">
<h3 id="org5e47047"><span class="section-number-3">1.4</span> Printers</h3>
<div id="outline-container-org8f61c62" class="outline-3">
<h3 id="org8f61c62"><span class="section-number-3">1.4</span> Printers</h3>
<div class="outline-text-3" id="text-1-4">
<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
@ -418,24 +418,24 @@ Data structure which contains the number of &alpha; and &beta; electrons.
</div>
</div>
<div id="outline-container-orgc347c9f" class="outline-3">
<h3 id="orgc347c9f"><span class="section-number-3">1.5</span> Tests</h3>
<div id="outline-container-org0d76e84" class="outline-3">
<h3 id="org0d76e84"><span class="section-number-3">1.5</span> Tests</h3>
</div>
</div>
<div id="outline-container-org25852ad" class="outline-2">
<h2 id="org25852ad"><span class="section-number-2">2</span> Element</h2>
<div id="outline-container-org904d88b" class="outline-2">
<h2 id="org904d88b"><span class="section-number-2">2</span> Element</h2>
<div class="outline-text-2" id="text-2">
<p>
Chemical elements.
</p>
</div>
<div id="outline-container-org038a472" class="outline-3">
<h3 id="org038a472"><span class="section-number-3">2.1</span> Type</h3>
<div id="outline-container-org0f44138" class="outline-3">
<h3 id="org0f44138"><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="org124f3ea"><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="org5259e68"><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>
@ -452,8 +452,8 @@ Chemical elements.
</div>
</div>
<div id="outline-container-orgc0d1c8c" class="outline-3">
<h3 id="orgc0d1c8c"><span class="section-number-3">2.2</span> Conversion</h3>
<div id="outline-container-org3260b21" class="outline-3">
<h3 id="org3260b21"><span class="section-number-3">2.2</span> Conversion</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">of_string</span> <span class="org-tuareg-font-lock-operator">:</span> string <span class="org-tuareg-font-lock-operator">-&gt;</span> t
@ -514,7 +514,7 @@ Chemical elements.
</tbody>
</table>
<pre class="example" id="org227d844">
<pre class="example" id="org5a57380">
Element.of_string "Fe" ;;
- : Element.t = Particles.Element.Fe
@ -533,8 +533,8 @@ Element.(to_string Fe);;
</div>
</div>
<div id="outline-container-orgf48d5b6" class="outline-3">
<h3 id="orgf48d5b6"><span class="section-number-3">2.3</span> Database information</h3>
<div id="outline-container-orgecbb559" class="outline-3">
<h3 id="orgecbb559"><span class="section-number-3">2.3</span> Database information</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">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
@ -583,8 +583,8 @@ Element.(to_string Fe);;
</div>
</div>
<div id="outline-container-org4e97465" class="outline-3">
<h3 id="org4e97465"><span class="section-number-3">2.4</span> Printers</h3>
<div id="outline-container-org4204ce9" class="outline-3">
<h3 id="org4204ce9"><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
@ -595,30 +595,30 @@ Element.(to_string Fe);;
</div>
</div>
<div id="outline-container-org4c5689f" class="outline-2">
<h2 id="org4c5689f"><span class="section-number-2">3</span> Atomic mass</h2>
<div id="outline-container-orgc37ce9d" class="outline-2">
<h2 id="orgc37ce9d"><span class="section-number-2">3</span> Atomic mass</h2>
<div class="outline-text-2" id="text-3">
<p>
Atomic mass, a non-negative float.
</p>
<div class="org-src-container">
<pre class="src src-ocaml" id="orgb624991"><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="org0e1101a"><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-org6bd3bbb" class="outline-2">
<h2 id="org6bd3bbb"><span class="section-number-2">4</span> Nuclei</h2>
<div id="outline-container-org485ac9f" class="outline-2">
<h2 id="org485ac9f"><span class="section-number-2">4</span> Nuclei</h2>
<div class="outline-text-2" id="text-4">
</div>
<div id="outline-container-org91c1c84" class="outline-3">
<h3 id="org91c1c84"><span class="section-number-3">4.1</span> Type</h3>
<div id="outline-container-org02f7836" class="outline-3">
<h3 id="org02f7836"><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" id="org3d3e724"><span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Common</span>
<pre class="src src-ocaml" id="org29d788e"><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>
@ -626,12 +626,12 @@ Atomic mass, a non-negative float.
</div>
</div>
<div id="outline-container-org0e06d85" class="outline-3">
<h3 id="org0e06d85"><span class="section-number-3">4.2</span> xyz file lexer/parser</h3>
<div id="outline-container-orgfdafdd0" class="outline-3">
<h3 id="orgfdafdd0"><span class="section-number-3">4.2</span> xyz file lexer/parser</h3>
<div class="outline-text-3" id="text-4-2">
</div>
<div id="outline-container-orgd2a815e" class="outline-4">
<h4 id="orgd2a815e"><span class="section-number-4">4.2.1</span> Lexer</h4>
<div id="outline-container-orgeddfd39" class="outline-4">
<h4 id="orgeddfd39"><span class="section-number-4">4.2.1</span> Lexer</h4>
<div class="outline-text-4" id="text-4-2-1">
<p>
<code>nuclei_lexer.mll</code> contains the description of the lexemes used in
@ -684,8 +684,8 @@ rule read_all <span class="org-tuareg-font-lock-operator">=</span> parse
</div>
</div>
<div id="outline-container-orga0e9364" class="outline-4">
<h4 id="orga0e9364"><span class="section-number-4">4.2.2</span> Parser</h4>
<div id="outline-container-orgb1e9400" class="outline-4">
<h4 id="orgb1e9400"><span class="section-number-4">4.2.2</span> Parser</h4>
<div class="outline-text-4" id="text-4-2-2">
<p>
<code>xyz_parser.mly</code> parses nuclear coordinates in xyz format.
@ -804,8 +804,8 @@ an <code>xyz_file</code> data structure.
</div>
</div>
<div id="outline-container-org67c4576" class="outline-3">
<h3 id="org67c4576"><span class="section-number-3">4.3</span> Conversion</h3>
<div id="outline-container-org19995b8" class="outline-3">
<h3 id="org19995b8"><span class="section-number-3">4.3</span> Conversion</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">of_xyz_string</span> <span class="org-tuareg-font-lock-operator">:</span> string <span class="org-tuareg-font-lock-operator">-&gt;</span> t
@ -864,8 +864,8 @@ an <code>xyz_file</code> data structure.
</div>
</div>
<div id="outline-container-org31c8415" class="outline-3">
<h3 id="org31c8415"><span class="section-number-3">4.4</span> <span class="todo TODO">TODO</span> Query</h3>
<div id="outline-container-org57fb733" class="outline-3">
<h3 id="org57fb733"><span class="section-number-3">4.4</span> <span class="todo TODO">TODO</span> Query</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">formula</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> string
@ -914,8 +914,8 @@ an <code>xyz_file</code> data structure.
</div>
</div>
<div id="outline-container-orga01f8b6" class="outline-3">
<h3 id="orga01f8b6"><span class="section-number-3">4.5</span> Printers</h3>
<div id="outline-container-org87456a6" class="outline-3">
<h3 id="org87456a6"><span class="section-number-3">4.5</span> Printers</h3>
<div class="outline-text-3" id="text-4-5">
<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
@ -924,31 +924,31 @@ an <code>xyz_file</code> data structure.
</div>
</div>
<div id="outline-container-orgf2e9bac" class="outline-3">
<h3 id="orgf2e9bac"><span class="section-number-3">4.6</span> Tests</h3>
<div id="outline-container-org60012a5" class="outline-3">
<h3 id="org60012a5"><span class="section-number-3">4.6</span> Tests</h3>
</div>
</div>
<div id="outline-container-org3573ea4" class="outline-2">
<h2 id="org3573ea4"><span class="section-number-2">5</span> Z-matrix</h2>
<div id="outline-container-org72daeec" class="outline-2">
<h2 id="org72daeec"><span class="section-number-2">5</span> Z-matrix</h2>
<div class="outline-text-2" id="text-5">
<p>
Z-matrix representation of nuclear coordinates.
</p>
</div>
<div id="outline-container-org7593a50" class="outline-3">
<h3 id="org7593a50"><span class="section-number-3">5.1</span> Type</h3>
<div id="outline-container-org0859680" class="outline-3">
<h3 id="org0859680"><span class="section-number-3">5.1</span> Type</h3>
<div class="outline-text-3" id="text-5-1">
<div class="org-src-container">
<pre class="src src-ocaml" id="org742f0bb"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span>
<pre class="src src-ocaml" id="org45ef285"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span>
</pre>
</div>
</div>
</div>
<div id="outline-container-orgf0cdae8" class="outline-3">
<h3 id="orgf0cdae8"><span class="section-number-3">5.2</span> Conversion</h3>
<div id="outline-container-org9ab67d9" class="outline-3">
<h3 id="org9ab67d9"><span class="section-number-3">5.2</span> Conversion</h3>
<div class="outline-text-3" id="text-5-2">
<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
@ -983,7 +983,7 @@ Z-matrix representation of nuclear coordinates.
</tbody>
</table>
<pre class="example" id="org22200dd">
<pre class="example" id="org802a2a2">
let zmt = Zmatrix.of_string "
n
n 1 nn
@ -1028,8 +1028,8 @@ H -0.568803 -0.793910 1.726048"
</div>
<div id="outline-container-org08080f5" class="outline-3">
<h3 id="org08080f5"><span class="section-number-3">5.3</span> Printers</h3>
<div id="outline-container-org442f12d" class="outline-3">
<h3 id="org442f12d"><span class="section-number-3">5.3</span> Printers</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">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
@ -1041,7 +1041,7 @@ H -0.568803 -0.793910 1.726048"
</div>
<div id="postamble" class="status">
<p class="author">Author: Anthony Scemama</p>
<p class="date">Created: 2021-01-01 Fri 16:37</p>
<p class="date">Created: 2021-01-01 Fri 17:04</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

46
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>
<!-- 2021-01-01 Fri 16:38 -->
<!-- 2021-01-01 Fri 17:04 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Perturbation</title>
@ -229,31 +229,31 @@
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org4a19d89">1. MP2</a>
<li><a href="#orgb7db984">1. MP2</a>
<ul>
<li><a href="#org9ac9790">1.1. Type</a></li>
<li><a href="#org0b288bd">1.2. Creation</a></li>
<li><a href="#org0bf5c08">1.3. Access</a></li>
<li><a href="#org10bdc37">1.4. Printers</a></li>
<li><a href="#org38093b0">1.5. Tests</a></li>
<li><a href="#orgde4eab7">1.1. Type</a></li>
<li><a href="#org7f0395b">1.2. Creation</a></li>
<li><a href="#org608f955">1.3. Access</a></li>
<li><a href="#orgae3f871">1.4. Printers</a></li>
<li><a href="#orge5d4a5e">1.5. Tests</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div class="org-src-container">
<pre class="src src-ocaml" id="org8cc608d"><span class="org-string">"Perturbation theory"</span>
<pre class="src src-ocaml" id="orgefa02b2"><span class="org-string">"Perturbation theory"</span>
</pre>
</div>
<div id="outline-container-org4a19d89" class="outline-2">
<h2 id="org4a19d89"><span class="section-number-2">1</span> MP2</h2>
<div id="outline-container-orgb7db984" class="outline-2">
<h2 id="orgb7db984"><span class="section-number-2">1</span> MP2</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-org9ac9790" class="outline-3">
<h3 id="org9ac9790"><span class="section-number-3">1.1</span> Type</h3>
<div id="outline-container-orgde4eab7" class="outline-3">
<h3 id="orgde4eab7"><span class="section-number-3">1.1</span> Type</h3>
<div class="outline-text-3" id="text-1-1">
<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>
@ -262,8 +262,8 @@
</div>
</div>
<div id="outline-container-org0b288bd" class="outline-3">
<h3 id="org0b288bd"><span class="section-number-3">1.2</span> Creation</h3>
<div id="outline-container-org7f0395b" class="outline-3">
<h3 id="org7f0395b"><span class="section-number-3">1.2</span> Creation</h3>
<div class="outline-text-3" id="text-1-2">
<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
@ -286,7 +286,7 @@
</tbody>
</table>
<pre class="example" id="org3955144">
<pre class="example" id="org483a232">
let mp2 =
Mp2.make ~frozen_core:(Mo.Frozen_core.(make Small molecule)) mo_basis
;;
@ -295,8 +295,8 @@ let mp2 =
</div>
</div>
<div id="outline-container-org0bf5c08" class="outline-3">
<h3 id="org0bf5c08"><span class="section-number-3">1.3</span> Access</h3>
<div id="outline-container-org608f955" class="outline-3">
<h3 id="org608f955"><span class="section-number-3">1.3</span> Access</h3>
<div class="outline-text-3" id="text-1-3">
<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
@ -331,14 +331,14 @@ let mp2 =
</tbody>
</table>
<pre class="example" id="orgabe71c7">
<pre class="example" id="org85faf3f">
</pre>
</div>
</div>
<div id="outline-container-org10bdc37" class="outline-3">
<h3 id="org10bdc37"><span class="section-number-3">1.4</span> Printers</h3>
<div id="outline-container-orgae3f871" class="outline-3">
<h3 id="orgae3f871"><span class="section-number-3">1.4</span> Printers</h3>
<div class="outline-text-3" id="text-1-4">
<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
@ -347,14 +347,14 @@ let mp2 =
</div>
</div>
<div id="outline-container-org38093b0" class="outline-3">
<h3 id="org38093b0"><span class="section-number-3">1.5</span> Tests</h3>
<div id="outline-container-orge5d4a5e" class="outline-3">
<h3 id="orge5d4a5e"><span class="section-number-3">1.5</span> Tests</h3>
</div>
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: Anthony Scemama</p>
<p class="date">Created: 2021-01-01 Fri 16:38</p>
<p class="date">Created: 2021-01-01 Fri 17:04</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

239
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@ -0,0 +1,239 @@
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<body>
<div id="content">
<h1 class="title">QCaml</h1>
<div class="org-src-container">
<pre class="src src-ocaml" id="org8035ba4"><span class="org-string">"Main QCaml entry point"</span>
</pre>
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: Anthony Scemama</p>
<p class="date">Created: 2021-01-01 Fri 17:04</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>
</html>

40
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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>
<!-- 2021-01-01 Fri 16:38 -->
<!-- 2021-01-01 Fri 17:04 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Simulation</title>
@ -229,50 +229,50 @@
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgf303bc5">1. Simulation</a>
<li><a href="#orge9e6843">1. Simulation</a>
<ul>
<li><a href="#org2e878c8">1.1. Type</a></li>
<li><a href="#org0ad2cbd">1.2. Access</a></li>
<li><a href="#orgee1bf18">1.3. Creation</a></li>
<li><a href="#org7e516a7">1.4. Printers</a></li>
<li><a href="#org33ea513">1.1. Type</a></li>
<li><a href="#org191cd92">1.2. Access</a></li>
<li><a href="#org55a5a12">1.3. Creation</a></li>
<li><a href="#org54162e7">1.4. Printers</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div class="org-src-container">
<pre class="src src-ocaml" id="orgd63cdb3"><span class="org-string">"Data describing a simulation (AOs, operators, nuclear coordinate,...)"</span>
<pre class="src src-ocaml" id="orga2f4cb7"><span class="org-string">"Data describing a simulation (AOs, operators, nuclear coordinate,...)"</span>
</pre>
</div>
<div id="outline-container-orgf303bc5" class="outline-2">
<h2 id="orgf303bc5"><span class="section-number-2">1</span> Simulation</h2>
<div id="outline-container-orge9e6843" class="outline-2">
<h2 id="orge9e6843"><span class="section-number-2">1</span> Simulation</h2>
<div class="outline-text-2" id="text-1">
<p>
Contains the state of the simulation.
</p>
<div class="org-src-container">
<pre class="src src-ocaml" id="orgb80da13"><span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Common</span>
<pre class="src src-ocaml" id="orgd14f732"><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">open </span><span class="org-tuareg-font-lock-module">Particles</span>
<span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Operators</span>
</pre>
</div>
</div>
<div id="outline-container-org2e878c8" class="outline-3">
<h3 id="org2e878c8"><span class="section-number-3">1.1</span> Type</h3>
<div id="outline-container-org33ea513" class="outline-3">
<h3 id="org33ea513"><span class="section-number-3">1.1</span> Type</h3>
<div class="outline-text-3" id="text-1-1">
<div class="org-src-container">
<pre class="src src-ocaml" id="orgd92e1cd"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span>
<pre class="src src-ocaml" id="org69769ce"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span>
</pre>
</div>
</div>
</div>
<div id="outline-container-org0ad2cbd" class="outline-3">
<h3 id="org0ad2cbd"><span class="section-number-3">1.2</span> Access</h3>
<div id="outline-container-org191cd92" class="outline-3">
<h3 id="org191cd92"><span class="section-number-3">1.2</span> Access</h3>
<div class="outline-text-3" id="text-1-2">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">nuclei</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">Nuclei.</span>t
@ -327,8 +327,8 @@ Contains the state of the simulation.
</div>
</div>
<div id="outline-container-orgee1bf18" class="outline-3">
<h3 id="orgee1bf18"><span class="section-number-3">1.3</span> Creation</h3>
<div id="outline-container-org55a5a12" class="outline-3">
<h3 id="org55a5a12"><span class="section-number-3">1.3</span> Creation</h3>
<div class="outline-text-3" id="text-1-3">
<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">?multiplicity</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-label">?charge</span><span class="org-tuareg-font-lock-operator">:</span>int <span class="org-tuareg-font-lock-operator">-&gt;</span>
@ -348,8 +348,8 @@ Defaults:
</div>
</div>
<div id="outline-container-org7e516a7" class="outline-3">
<h3 id="org7e516a7"><span class="section-number-3">1.4</span> Printers</h3>
<div id="outline-container-org54162e7" class="outline-3">
<h3 id="org54162e7"><span class="section-number-3">1.4</span> Printers</h3>
<div class="outline-text-3" id="text-1-4">
<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
@ -361,7 +361,7 @@ Defaults:
</div>
<div id="postamble" class="status">
<p class="author">Author: Anthony Scemama</p>
<p class="date">Created: 2021-01-01 Fri 16:38</p>
<p class="date">Created: 2021-01-01 Fri 17:04</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

239
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@ -0,0 +1,239 @@
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<body>
<div id="content">
<h1 class="title">Top-level</h1>
<div class="org-src-container">
<pre class="src src-ocaml" id="orgf94ff09"><span class="org-string">"Installs pretty printers for top-level."</span>
</pre>
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: Anthony Scemama</p>
<p class="date">Created: 2021-01-01 Fri 17:04</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>
</html>

2
gaussian/README.org
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@ -1,5 +1,5 @@
#+TITLE: Gaussian
#+SETUPFILE: https://fniessen.github.io/org-html-themes/org/theme-readtheorg.setup
#+SETUPFILE: ../docs/org-html-themes/org/theme-readtheorg.setup
#+name: synopsis
#+begin_src ocaml :export output raw

2
gaussian_integrals/README.org
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@ -1,5 +1,5 @@
#+TITLE: Gaussian integrals
#+SETUPFILE: https://fniessen.github.io/org-html-themes/org/theme-readtheorg.setup
#+SETUPFILE: ../docs/org-html-themes/org/theme-readtheorg.setup
#+name: synopsis
#+begin_src ocaml :export output raw

2
linear_algebra/README.org
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@ -1,5 +1,5 @@
#+TITLE: Linear Algebra
#+SETUPFILE: https://fniessen.github.io/org-html-themes/org/theme-readtheorg.setup
#+SETUPFILE: ../docs/org-html-themes/org/theme-readtheorg.setup
#+name: synopsis
#+begin_src ocaml :export output raw

2
mo/README.org
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@ -1,5 +1,5 @@
#+TITLE: Molecular orbitals
#+SETUPFILE: https://fniessen.github.io/org-html-themes/org/theme-readtheorg.setup
#+SETUPFILE: ../docs/org-html-themes/org/theme-readtheorg.setup
#+name: synopsis
#+begin_src ocaml :export output raw

2
operators/README.org
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@ -1,5 +1,5 @@
#+TITLE: Operators
#+SETUPFILE: https://fniessen.github.io/org-html-themes/org/theme-readtheorg.setup
#+SETUPFILE: ../docs/org-html-themes/org/theme-readtheorg.setup
#+name: synopsis
#+begin_src ocaml :export output raw

2
particles/README.org
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@ -1,5 +1,5 @@
#+TITLE: Common
#+SETUPFILE: https://fniessen.github.io/org-html-themes/org/theme-readtheorg.setup
#+SETUPFILE: ../docs/org-html-themes/org/theme-readtheorg.setup
#+name: synopsis
#+begin_src ocaml :export output raw

2
perturbation/README.org
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@ -1,5 +1,5 @@
#+TITLE: Perturbation
#+SETUPFILE: https://fniessen.github.io/org-html-themes/org/theme-readtheorg.setup
#+SETUPFILE: ../docs/org-html-themes/org/theme-readtheorg.setup
#+name: synopsis
#+begin_src ocaml :export output raw

2
qcaml/README.org
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@ -1,5 +1,5 @@
#+TITLE: QCaml
#+SETUPFILE: https://fniessen.github.io/org-html-themes/org/theme-readtheorg.setup
#+SETUPFILE: ../docs/org-html-themes/org/theme-readtheorg.setup
#+name: synopsis
#+begin_src ocaml :export output raw

2
simulation/README.org
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@ -1,5 +1,5 @@
#+TITLE: Simulation
#+SETUPFILE: https://fniessen.github.io/org-html-themes/org/theme-readtheorg.setup
#+SETUPFILE: ../docs/org-html-themes/org/theme-readtheorg.setup
#+name: synopsis
#+begin_src ocaml :export output raw

6
top/README.org
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@ -1,5 +1,5 @@
#+TITLE: Top-level
#+SETUPFILE: https://fniessen.github.io/org-html-themes/org/theme-readtheorg.setup
#+SETUPFILE: ../docs/org-html-themes/org/theme-readtheorg.setup
#+name: synopsis
@ -19,15 +19,13 @@
#+header: :noweb strip-export
#+header: :var name=(file-name-directory buffer-file-name)
#+header: :var dune="lib/dune"
#+header: :var dunetest="test/dune"
#+begin_src python :exports none :results output none
name = name.split('/')[-2]
synopsis = """
<<synopsis>>
"""
with open(dune,'w') as f:
with open("lib/dune",'w') as f:
f.write(f"""
(library
(name {name})

11
top/install_printers.org
View File

@ -9,17 +9,18 @@
(org-babel-tangle)
#+end_src
* Intall printers
* Intall printers :noexport:
:PROPERTIES:
:header-args: :noweb yes :comments both
:END:
Installs printers in the top-level environment.
All printers are fetched automatically using the following script:
All printers are fetched automatically.
#+NAME: raw_printers
#+begin_src sh :results output raw
#+begin_src sh :results output raw :exports none
grep "val pp " ../*/*.org \
| grep -v docs \
| cut -d ":" -f 1 \
@ -32,7 +33,7 @@ grep "val pp " ../*/*.org \
#+end_src
#+NAME: printers
#+begin_src python :results output raw :var p=raw_printers
#+begin_src python :results output raw :var p=raw_printers :exports none
result = []
for l in p.split():
dir, module = l.split('.')
@ -45,6 +46,7 @@ result = '\n'.join(result)
print(result)
#+end_src
#+begin_src ocaml :tangle (eval ml) :exports none
let printers =
@ -69,4 +71,3 @@ let () =
Format.eprintf "Problem installing QCaml-printers@."
#+end_src