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<body>
<div id="org-div-home-and-up">
<a accesskey="h" href=""> UP </a>
|
<a accesskey="H" href="index.html"> HOME </a>
</div><div id="content">
<h1 class="title">Common</h1>
<div id="table-of-contents">
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org6df3964">1. Summary</a></li>
<li><a href="#org5753373">2. Electrons</a>
<ul>
<li><a href="#org25fbdd2">2.1. Type</a></li>
<li><a href="#org5d0f6c5">2.2. Creation</a></li>
<li><a href="#org6c90a8b">2.3. Access</a></li>
<li><a href="#orgd40dbf2">2.4. Printers</a></li>
<li><a href="#org20072b6">2.5. Tests</a></li>
</ul>
</li>
<li><a href="#orgb411aa8">3. Element</a>
<ul>
<li><a href="#org7b29939">3.1. Type</a></li>
<li><a href="#org46b8b47">3.2. Conversion</a></li>
<li><a href="#org1d70546">3.3. Database information</a></li>
<li><a href="#orgd5738cc">3.4. Printers</a></li>
</ul>
</li>
<li><a href="#org61359db">4. Atomic mass</a></li>
<li><a href="#org3653358">5. Nuclei</a>
<ul>
<li><a href="#orgdc5c638">5.1. Type</a></li>
<li><a href="#org795558e">5.2. xyz file lexer/parser</a>
<ul>
<li><a href="#orgfa3e0b9">5.2.1. Lexer</a></li>
<li><a href="#orge4240df">5.2.2. Parser</a></li>
</ul>
</li>
<li><a href="#orgfe57c35">5.3. Conversion</a></li>
<li><a href="#org14de381">5.4. Query</a></li>
<li><a href="#org9224cc6">5.5. TREXIO</a>
<ul>
<li><a href="#org7046b2a">5.5.1. Read</a></li>
<li><a href="#orgd1b3675">5.5.2. Write</a></li>
</ul>
</li>
<li><a href="#org3ece660">5.6. Printers</a></li>
<li><a href="#org6a90479">5.7. Tests</a></li>
</ul>
</li>
<li><a href="#org46003da">6. Z-matrix</a>
<ul>
<li><a href="#org5fcb7ed">6.1. Type</a></li>
<li><a href="#orga6c6d0e">6.2. Conversion</a></li>
<li><a href="#org37a7c2e">6.3. Printers</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org6df3964" class="outline-2">
<h2 id="org6df3964"><span class="section-number-2">1</span> Summary</h2>
</div>
<div id="outline-container-org5753373" class="outline-2">
<h2 id="org5753373"><span class="section-number-2">2</span> Electrons</h2>
<div class="outline-text-2" id="text-2">
<p>
Data structure which contains the number of &alpha; and &beta; electrons.
</p>
</div>
<div id="outline-container-org25fbdd2" class="outline-3">
<h3 id="org25fbdd2"><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="org59c86ec"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span>
</pre>
</div>
</div>
</div>
<div id="outline-container-org5d0f6c5" class="outline-3">
<h3 id="org5d0f6c5"><span class="section-number-3">2.2</span> Creation</h3>
<div class="outline-text-3" id="text-2-2">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Common</span>
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">make</span> <span class="org-tuareg-font-lock-operator">:</span> int <span class="org-tuareg-font-lock-operator">-&gt;</span> int <span class="org-tuareg-font-lock-operator">-&gt;</span> t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">of_atoms</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> <span class="org-tuareg-font-lock-module">Nuclei.</span>t <span class="org-tuareg-font-lock-operator">-&gt;</span> t
<span class="org-comment-delimiter">(* </span><span class="org-comment">@param multiplicity default is 1</span>
<span class="org-comment"> @param charge default is 0</span>
<span class="org-comment"> @raise Invalid_argument if the spin multiplicity is not compatible with</span>
<span class="org-comment"> the molecule and the total charge.</span>
<span class="org-comment-delimiter">*)</span>
</pre>
</div>
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
<col class="org-left" />
<col class="org-left" />
</colgroup>
<tbody>
<tr>
<td class="org-left"><code>make</code></td>
<td class="org-left"><code>make n_alfa n_beta</code></td>
</tr>
<tr>
<td class="org-left"><code>of_atoms</code></td>
<td class="org-left">Creates the data relative to electrons for a molecular system described by <a href="#org1056889"><code>Nuclei.t</code></a> for a given total charge and spin multiplicity.</td>
</tr>
</tbody>
</table>
</div>
</div>
<div id="outline-container-org6c90a8b" class="outline-3">
<h3 id="org6c90a8b"><span class="section-number-3">2.3</span> Access</h3>
<div class="outline-text-3" id="text-2-3">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">charge</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Charge.</span>t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">n_elec</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> int
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">n_alfa</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> int
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">n_beta</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> int
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">multiplicity</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> int
</pre>
</div>
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
<col class="org-left" />
<col class="org-left" />
</colgroup>
<tbody>
<tr>
<td class="org-left"><code>charge</code></td>
<td class="org-left">Sum of the charges of the electrons</td>
</tr>
<tr>
<td class="org-left"><code>n_elec</code></td>
<td class="org-left">Number of electrons</td>
</tr>
<tr>
<td class="org-left"><code>n_alfa</code></td>
<td class="org-left">Number of alpha electrons</td>
</tr>
<tr>
<td class="org-left"><code>n_beta</code></td>
<td class="org-left">Number of beta electrons</td>
</tr>
<tr>
<td class="org-left"><code>multiplicity</code></td>
<td class="org-left">Spin multiplicity: \(2S+1\)</td>
</tr>
</tbody>
</table>
</div>
</div>
<div id="outline-container-orgd40dbf2" class="outline-3">
<h3 id="orgd40dbf2"><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
</pre>
</div>
</div>
</div>
<div id="outline-container-org20072b6" class="outline-3">
<h3 id="org20072b6"><span class="section-number-3">2.5</span> Tests</h3>
</div>
</div>
<div id="outline-container-orgb411aa8" class="outline-2">
<h2 id="orgb411aa8"><span class="section-number-2">3</span> Element</h2>
<div class="outline-text-2" id="text-3">
<p>
Chemical elements.
</p>
</div>
<div id="outline-container-org7b29939" class="outline-3">
<h3 id="org7b29939"><span class="section-number-3">3.1</span> Type</h3>
<div class="outline-text-3" id="text-3-1">
<div class="org-src-container">
<pre class="src src-ocaml" id="org088d0e5"><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>
<span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Na</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Mg</span> <span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Al</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Si</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">P</span> <span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">S</span> <span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Cl</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Ar</span>
<span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">K</span> <span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Ca</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Sc</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Ti</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">V</span> <span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Cr</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Mn</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Fe</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Co</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Ni</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Cu</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Zn</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Ga</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Ge</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">As</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Se</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Br</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Kr</span>
<span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Rb</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Sr</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Y</span> <span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Zr</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Nb</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Mo</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Tc</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Ru</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Rh</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Pd</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Ag</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Cd</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">In</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Sn</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Sb</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Te</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">I</span> <span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Xe</span>
<span class="org-tuareg-font-lock-operator">|</span><span class="org-tuareg-font-lock-constructor">Pt</span>
<span class="org-keyword">exception</span> <span class="org-tuareg-font-lock-constructor">ElementError</span> <span class="org-keyword">of</span> string
<span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Common</span>
</pre>
</div>
</div>
</div>
<div id="outline-container-org46b8b47" class="outline-3">
<h3 id="org46b8b47"><span class="section-number-3">3.2</span> Conversion</h3>
<div class="outline-text-3" id="text-3-2">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">of_string</span> <span class="org-tuareg-font-lock-operator">:</span> string <span class="org-tuareg-font-lock-operator">-&gt;</span> t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">to_string</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> string
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">to_long_string</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> string
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">to_int</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> int
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">of_int</span> <span class="org-tuareg-font-lock-operator">:</span> int <span class="org-tuareg-font-lock-operator">-&gt;</span> t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">to_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
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">of_charge</span> <span class="org-tuareg-font-lock-operator">:</span> <span class="org-tuareg-font-lock-module">Charge.</span>t <span class="org-tuareg-font-lock-operator">-&gt;</span> t
</pre>
</div>
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
<col class="org-left" />
<col class="org-left" />
</colgroup>
<tbody>
<tr>
<td class="org-left"><code>of_string</code></td>
<td class="org-left">Creates an <code>Element.t</code> from a chemical symbol or from the full name of the element (case insensitive)</td>
</tr>
<tr>
<td class="org-left"><code>to_string</code></td>
<td class="org-left">Gets the chemical symbol of the <code>Element.t</code> in a string</td>
</tr>
<tr>
<td class="org-left"><code>to_long_string</code></td>
<td class="org-left">Gets the full name of the <code>Element.t</code> in a string</td>
</tr>
<tr>
<td class="org-left"><code>to_int</code></td>
<td class="org-left">Convert to the atomic charge, with <code>int</code> type</td>
</tr>
<tr>
<td class="org-left"><code>of_int</code></td>
<td class="org-left">Create from the atomic charge, with <code>int</code> type</td>
</tr>
<tr>
<td class="org-left"><code>to_charge</code></td>
<td class="org-left">Convert to the atomic charge, with <code>Charge.t</code> type</td>
</tr>
<tr>
<td class="org-left"><code>of_charge</code></td>
<td class="org-left">Create from the atomic charge, with <code>Charge.t</code> type</td>
</tr>
</tbody>
</table>
<pre class="example" id="org3545bb2">
Element.of_string "Fe" ;;
- : Element.t = Particles.Element.Fe
Element.of_string "hydrogen" ;;
- : Element.t = Particles.Element.H
Element.of_string "Kryptonite" ;;
Exception: Particles.Element.ElementError "Element Kryptonite unknown".
Element.(to_long_string Fe) ;;
- : string = "Iron"
Element.(to_string Fe);;
- : string = "Fe"
</pre>
</div>
</div>
<div id="outline-container-org1d70546" class="outline-3">
<h3 id="org1d70546"><span class="section-number-3">3.3</span> Database information</h3>
<div class="outline-text-3" id="text-3-3">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">covalent_radius</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> <span class="org-tuareg-font-lock-module">Non_negative_float.</span>t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">vdw_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
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">mass</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">Mass.</span>t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">small_core</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> int
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">large_core</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> int
</pre>
</div>
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
<col class="org-left" />
<col class="org-left" />
</colgroup>
<tbody>
<tr>
<td class="org-left"><code>covalent_radius</code></td>
<td class="org-left">Covalent radii of the elements, in atomic units</td>
</tr>
<tr>
<td class="org-left"><code>vdw_radius</code></td>
<td class="org-left">Van der Waals radii of the elements, in atomic units</td>
</tr>
<tr>
<td class="org-left"><code>mass</code></td>
<td class="org-left">Atomic mass of the elements, in atomic units)</td>
</tr>
<tr>
<td class="org-left"><code>small_core</code></td>
<td class="org-left">Number of electrons in the small core model (all except the outermost two shells)</td>
</tr>
<tr>
<td class="org-left"><code>large_core</code></td>
<td class="org-left">Number of electrons in the large core model (all except the outermost shell)</td>
</tr>
</tbody>
</table>
</div>
</div>
<div id="outline-container-orgd5738cc" class="outline-3">
<h3 id="orgd5738cc"><span class="section-number-3">3.4</span> Printers</h3>
<div class="outline-text-3" id="text-3-4">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">pp</span> <span class="org-tuareg-font-lock-operator">:</span> <span class="org-tuareg-font-lock-module">Format.</span>formatter <span class="org-tuareg-font-lock-operator">-&gt;</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> unit
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">pp_long</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
</pre>
</div>
</div>
</div>
</div>
<div id="outline-container-org61359db" class="outline-2">
<h2 id="org61359db"><span class="section-number-2">4</span> Atomic mass</h2>
<div class="outline-text-2" id="text-4">
<p>
Atomic mass, a non-negative float.
</p>
<div class="org-src-container">
<pre class="src src-ocaml" id="orgff86835"><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-org3653358" class="outline-2">
<h2 id="org3653358"><span class="section-number-2">5</span> Nuclei</h2>
<div class="outline-text-2" id="text-5">
</div>
<div id="outline-container-orgdc5c638" class="outline-3">
<h3 id="orgdc5c638"><span class="section-number-3">5.1</span> Type</h3>
<div class="outline-text-3" id="text-5-1">
<p>
<a id="org1056889"><code>Nuclei.t</code></a>
</p>
<div class="org-src-container">
<pre class="src src-ocaml" id="org5d75f82"><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>
</div>
</div>
</div>
<div id="outline-container-org795558e" class="outline-3">
<h3 id="org795558e"><span class="section-number-3">5.2</span> xyz file lexer/parser</h3>
<div class="outline-text-3" id="text-5-2">
</div>
<div id="outline-container-orgfa3e0b9" class="outline-4">
<h4 id="orgfa3e0b9"><span class="section-number-4">5.2.1</span> Lexer</h4>
<div class="outline-text-4" id="text-5-2-1">
<p>
<code>nuclei_lexer.mll</code> contains the description of the lexemes used in
an xyz file.
</p>
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-operator">{</span>
<span class="org-tuareg-font-lock-governing">open </span><span class="org-tuareg-font-lock-module">Xyz_parser</span>
<span class="org-tuareg-font-lock-operator">}</span>
<span class="org-tuareg-font-lock-governing">let</span> <span class="org-variable-name">eol</span> <span class="org-tuareg-font-lock-operator">=</span> <span class="org-tuareg-font-lock-operator">[</span><span class="org-string">'\n'</span><span class="org-tuareg-font-lock-operator">]</span>
<span class="org-tuareg-font-lock-governing">let</span> <span class="org-variable-name">white</span> <span class="org-tuareg-font-lock-operator">=</span> <span class="org-tuareg-font-lock-operator">[</span><span class="org-string">' '</span> <span class="org-string">'\t'</span><span class="org-tuareg-font-lock-operator">]+</span>
<span class="org-tuareg-font-lock-governing">let</span> <span class="org-variable-name">word</span> <span class="org-tuareg-font-lock-operator">=</span> <span class="org-tuareg-font-lock-operator">[^</span><span class="org-string">' '</span> <span class="org-string">'\t'</span> <span class="org-string">'\n'</span><span class="org-tuareg-font-lock-operator">]+</span>
<span class="org-tuareg-font-lock-governing">let</span> <span class="org-variable-name">letter</span> <span class="org-tuareg-font-lock-operator">=</span> <span class="org-tuareg-font-lock-operator">[</span><span class="org-string">'A'</span><span class="org-tuareg-font-lock-operator">-</span><span class="org-string">'Z'</span> <span class="org-string">'a'</span><span class="org-tuareg-font-lock-operator">-</span><span class="org-string">'z'</span><span class="org-tuareg-font-lock-operator">]</span>
<span class="org-tuareg-font-lock-governing">let</span> <span class="org-variable-name">integer</span> <span class="org-tuareg-font-lock-operator">=</span> <span class="org-tuareg-font-lock-operator">[</span><span class="org-string">'0'</span><span class="org-tuareg-font-lock-operator">-</span><span class="org-string">'9'</span><span class="org-tuareg-font-lock-operator">]+</span>
<span class="org-tuareg-font-lock-governing">let</span> <span class="org-variable-name">real</span> <span class="org-tuareg-font-lock-operator">=</span> <span class="org-string">'-'</span><span class="org-tuareg-font-lock-operator">?</span> <span class="org-tuareg-font-lock-operator">(</span>integer <span class="org-string">'.'</span> integer <span class="org-tuareg-font-lock-operator">|</span> integer <span class="org-string">'.'</span> <span class="org-tuareg-font-lock-operator">|</span> <span class="org-string">'.'</span> integer<span class="org-tuareg-font-lock-operator">)</span> <span class="org-tuareg-font-lock-operator">([</span><span class="org-string">'e'</span> <span class="org-string">'E'</span><span class="org-tuareg-font-lock-operator">]</span> <span class="org-tuareg-font-lock-operator">(</span><span class="org-string">'+'</span><span class="org-tuareg-font-lock-operator">|</span><span class="org-string">'-'</span><span class="org-tuareg-font-lock-operator">)?</span> integer<span class="org-tuareg-font-lock-operator">)?</span>
rule read_all <span class="org-tuareg-font-lock-operator">=</span> parse
<span class="org-tuareg-font-lock-operator">|</span> eof <span class="org-tuareg-font-lock-operator">{</span> <span class="org-tuareg-font-lock-constructor">EOF</span> <span class="org-tuareg-font-lock-operator">}</span>
<span class="org-tuareg-font-lock-operator">|</span> eol <span class="org-tuareg-font-lock-operator">{</span> <span class="org-tuareg-font-lock-constructor">EOL</span> <span class="org-tuareg-font-lock-operator">}</span>
<span class="org-tuareg-font-lock-operator">|</span> white <span class="org-keyword">as</span> w <span class="org-tuareg-font-lock-operator">{</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> w <span class="org-tuareg-font-lock-operator">}</span>
<span class="org-tuareg-font-lock-operator">|</span> integer <span class="org-keyword">as</span> i <span class="org-tuareg-font-lock-operator">{</span> <span class="org-tuareg-font-lock-constructor">INTEGER</span> <span class="org-tuareg-font-lock-operator">(</span>int_of_string i<span class="org-tuareg-font-lock-operator">)</span> <span class="org-tuareg-font-lock-operator">}</span>
<span class="org-tuareg-font-lock-operator">|</span> real <span class="org-keyword">as</span> f <span class="org-tuareg-font-lock-operator">{</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-operator">(</span>float_of_string f<span class="org-tuareg-font-lock-operator">)</span> <span class="org-tuareg-font-lock-operator">}</span>
<span class="org-tuareg-font-lock-operator">|</span> word <span class="org-keyword">as</span> w <span class="org-tuareg-font-lock-operator">{</span> <span class="org-tuareg-font-lock-constructor">WORD</span> w <span class="org-tuareg-font-lock-operator">}</span>
<span class="org-tuareg-font-lock-operator">{</span>
<span class="org-comment-delimiter">(* </span><span class="org-comment">DEBUG</span>
<span class="org-comment"> let () =</span>
<span class="org-comment"> let ic = open_in "h2o.xyz" in</span>
<span class="org-comment"> let lexbuf = Lexing.from_channel ic in</span>
<span class="org-comment"> while true do</span>
<span class="org-comment"> let s =</span>
<span class="org-comment"> match read_all lexbuf with</span>
<span class="org-comment"> | EOL -&gt; "EOL"</span>
<span class="org-comment"> | SPACE w -&gt; "SPACE("^w^")"</span>
<span class="org-comment"> | INTEGER i -&gt; "INTEGER("^(string_of_int i)^")"</span>
<span class="org-comment"> | FLOAT f -&gt; "FLOAT("^(string_of_float f)^")"</span>
<span class="org-comment"> | WORD w -&gt; "WORD("^w^")"</span>
<span class="org-comment"> | EOF -&gt; "EOF"</span>
<span class="org-comment"> in</span>
<span class="org-comment"> print_endline s</span>
<span class="org-comment"> done;</span>
<span class="org-comment-delimiter">*)</span>
<span class="org-tuareg-font-lock-operator">}</span>
</pre>
</div>
</div>
</div>
<div id="outline-container-orge4240df" class="outline-4">
<h4 id="orge4240df"><span class="section-number-4">5.2.2</span> Parser</h4>
<div class="outline-text-4" id="text-5-2-2">
<p>
<code>xyz_parser.mly</code> parses nuclear coordinates in xyz format.
</p>
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-operator">%{</span>
<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">let</span> <span class="org-function-name">make_angstrom</span><span class="org-variable-name"> x y z</span> <span class="org-tuareg-font-lock-operator">=</span>
<span class="org-tuareg-font-lock-module">Coordinate.</span><span class="org-tuareg-font-lock-operator">(</span>make_angstrom <span class="org-tuareg-font-lock-operator">{</span>
x <span class="org-tuareg-font-lock-operator">;</span> y <span class="org-tuareg-font-lock-operator">;</span> z
<span class="org-tuareg-font-lock-operator">})</span>
<span class="org-tuareg-font-lock-governing">let</span> <span class="org-function-name">output_of</span><span class="org-variable-name"> f x y z</span> <span class="org-tuareg-font-lock-operator">=</span>
<span class="org-tuareg-font-lock-governing">let</span> <span class="org-variable-name">a</span> <span class="org-tuareg-font-lock-operator">=</span> make_angstrom x y z <span class="org-tuareg-font-lock-governing">in</span>
<span class="org-keyword">fun</span> <span class="org-variable-name">e</span> <span class="org-tuareg-font-lock-operator">-&gt;</span>
<span class="org-tuareg-font-lock-operator">{</span>
<span class="org-tuareg-font-lock-module">Xyz_ast.</span>
element <span class="org-tuareg-font-lock-operator">=</span> f e<span class="org-tuareg-font-lock-operator">;</span>
coord <span class="org-tuareg-font-lock-operator">=</span> a <span class="org-tuareg-font-lock-operator">;</span>
<span class="org-tuareg-font-lock-operator">}</span>
<span class="org-tuareg-font-lock-governing">let</span> <span class="org-variable-name">output_of_string</span> <span class="org-tuareg-font-lock-operator">=</span> output_of <span class="org-tuareg-font-lock-module">Element.</span>of_string
<span class="org-tuareg-font-lock-governing">let</span> <span class="org-variable-name">output_of_int</span> <span class="org-tuareg-font-lock-operator">=</span> output_of <span class="org-tuareg-font-lock-module">Element.</span>of_int
<span class="org-tuareg-font-lock-operator">%}</span>
<span class="org-tuareg-font-lock-operator">%</span>token <span class="org-tuareg-font-lock-constructor">EOL</span>
<span class="org-tuareg-font-lock-operator">%</span>token <span class="org-tuareg-font-lock-operator">&lt;</span>string<span class="org-tuareg-font-lock-operator">&gt;</span> <span class="org-tuareg-font-lock-constructor">SPACE</span>
<span class="org-tuareg-font-lock-operator">%</span>token <span class="org-tuareg-font-lock-operator">&lt;</span>string<span class="org-tuareg-font-lock-operator">&gt;</span> <span class="org-tuareg-font-lock-constructor">WORD</span>
<span class="org-tuareg-font-lock-operator">%</span>token <span class="org-tuareg-font-lock-operator">&lt;</span>int<span class="org-tuareg-font-lock-operator">&gt;</span> <span class="org-tuareg-font-lock-constructor">INTEGER</span>
<span class="org-tuareg-font-lock-operator">%</span>token <span class="org-tuareg-font-lock-operator">&lt;</span>float<span class="org-tuareg-font-lock-operator">&gt;</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span>
<span class="org-tuareg-font-lock-operator">%</span>token <span class="org-tuareg-font-lock-constructor">EOF</span>
<span class="org-tuareg-font-lock-operator">%</span>start input
<span class="org-tuareg-font-lock-operator">%</span><span class="org-tuareg-font-lock-governing">type</span> <span class="org-tuareg-font-lock-operator">&lt;</span><span class="org-tuareg-font-lock-module">Xyz_ast.</span>xyz_file<span class="org-tuareg-font-lock-operator">&gt;</span> input
<span class="org-tuareg-font-lock-operator">%%</span> <span class="org-tuareg-font-lock-operator">/*</span> <span class="org-tuareg-font-lock-constructor">Grammar</span> rules <span class="org-tuareg-font-lock-governing">and</span> <span class="org-function-name">actions</span><span class="org-variable-name"> follow</span> <span class="org-tuareg-font-lock-operator">*/</span>
input<span class="org-tuareg-font-lock-operator">:</span>
<span class="org-tuareg-font-lock-operator">|</span> integer title atoms_xyz <span class="org-tuareg-font-lock-operator">{</span>
<span class="org-tuareg-font-lock-operator">{</span>
number_of_atoms <span class="org-tuareg-font-lock-operator">=</span> $1<span class="org-tuareg-font-lock-operator">;</span>
file_title <span class="org-tuareg-font-lock-operator">=</span> $2<span class="org-tuareg-font-lock-operator">;</span>
nuclei <span class="org-tuareg-font-lock-operator">=</span> $3<span class="org-tuareg-font-lock-operator">;</span>
<span class="org-tuareg-font-lock-operator">}</span>
<span class="org-tuareg-font-lock-operator">}</span>
<span class="org-tuareg-font-lock-operator">;</span>
integer<span class="org-tuareg-font-lock-operator">:</span>
<span class="org-tuareg-font-lock-operator">|</span> <span class="org-tuareg-font-lock-constructor">INTEGER</span> <span class="org-tuareg-font-lock-constructor">EOL</span> <span class="org-tuareg-font-lock-operator">{</span> $1 <span class="org-tuareg-font-lock-operator">}</span>
<span class="org-tuareg-font-lock-operator">|</span> <span class="org-tuareg-font-lock-constructor">INTEGER</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">EOL</span> <span class="org-tuareg-font-lock-operator">{</span> $1 <span class="org-tuareg-font-lock-operator">}</span>
<span class="org-tuareg-font-lock-operator">|</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">INTEGER</span> <span class="org-tuareg-font-lock-constructor">EOL</span> <span class="org-tuareg-font-lock-operator">{</span> $2 <span class="org-tuareg-font-lock-operator">}</span>
<span class="org-tuareg-font-lock-operator">|</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">INTEGER</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">EOL</span> <span class="org-tuareg-font-lock-operator">{</span> $2 <span class="org-tuareg-font-lock-operator">}</span>
<span class="org-tuareg-font-lock-operator">;</span>
title<span class="org-tuareg-font-lock-operator">:</span>
<span class="org-tuareg-font-lock-operator">|</span> title_list <span class="org-tuareg-font-lock-constructor">EOL</span> <span class="org-tuareg-font-lock-operator">{</span> $1 <span class="org-tuareg-font-lock-operator">}</span>
<span class="org-tuareg-font-lock-operator">;</span>
text<span class="org-tuareg-font-lock-operator">:</span>
<span class="org-tuareg-font-lock-operator">|</span> <span class="org-tuareg-font-lock-constructor">WORD</span> <span class="org-tuareg-font-lock-operator">{</span> $1 <span class="org-tuareg-font-lock-operator">}</span>
<span class="org-tuareg-font-lock-operator">|</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-operator">{</span> $1 <span class="org-tuareg-font-lock-operator">}</span>
<span class="org-tuareg-font-lock-operator">|</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-operator">{</span> <span class="org-tuareg-font-lock-operator">(</span>string_of_float $1<span class="org-tuareg-font-lock-operator">)}</span>
<span class="org-tuareg-font-lock-operator">|</span> <span class="org-tuareg-font-lock-constructor">INTEGER</span> <span class="org-tuareg-font-lock-operator">{</span> <span class="org-tuareg-font-lock-operator">(</span>string_of_int $1<span class="org-tuareg-font-lock-operator">)}</span>
<span class="org-tuareg-font-lock-operator">;</span>
title_list<span class="org-tuareg-font-lock-operator">:</span>
<span class="org-tuareg-font-lock-operator">|</span> <span class="org-tuareg-font-lock-operator">{</span> <span class="org-string">""</span> <span class="org-tuareg-font-lock-operator">}</span>
<span class="org-tuareg-font-lock-operator">|</span> title_list text <span class="org-tuareg-font-lock-operator">{</span> <span class="org-tuareg-font-lock-operator">(</span>$1 <span class="org-tuareg-font-lock-operator">^</span> $2<span class="org-tuareg-font-lock-operator">)</span> <span class="org-tuareg-font-lock-operator">}</span>
<span class="org-tuareg-font-lock-operator">;</span>
atoms_xyz<span class="org-tuareg-font-lock-operator">:</span>
<span class="org-tuareg-font-lock-operator">|</span> atoms_list <span class="org-tuareg-font-lock-constructor">EOL</span> <span class="org-tuareg-font-lock-operator">{</span> <span class="org-tuareg-font-lock-module">List.</span>rev $1 <span class="org-tuareg-font-lock-operator">}</span>
<span class="org-tuareg-font-lock-operator">|</span> atoms_list <span class="org-tuareg-font-lock-constructor">EOF</span> <span class="org-tuareg-font-lock-operator">{</span> <span class="org-tuareg-font-lock-module">List.</span>rev $1 <span class="org-tuareg-font-lock-operator">}</span>
<span class="org-tuareg-font-lock-operator">;</span>
atoms_list<span class="org-tuareg-font-lock-operator">:</span>
<span class="org-tuareg-font-lock-operator">|</span> <span class="org-tuareg-font-lock-operator">{</span> <span class="org-tuareg-font-lock-operator">[]</span> <span class="org-tuareg-font-lock-operator">}</span>
<span class="org-tuareg-font-lock-operator">|</span> atoms_list <span class="org-tuareg-font-lock-constructor">WORD</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">EOL</span> <span class="org-tuareg-font-lock-operator">{</span> output_of_string $4 $6 $8 $2 <span class="org-tuareg-font-lock-operator">::</span> $1 <span class="org-tuareg-font-lock-operator">}</span>
<span class="org-tuareg-font-lock-operator">|</span> atoms_list <span class="org-tuareg-font-lock-constructor">WORD</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">EOL</span> <span class="org-tuareg-font-lock-operator">{</span> output_of_string $4 $6 $8 $2 <span class="org-tuareg-font-lock-operator">::</span> $1 <span class="org-tuareg-font-lock-operator">}</span>
<span class="org-tuareg-font-lock-operator">|</span> atoms_list <span class="org-tuareg-font-lock-constructor">INTEGER</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">EOL</span> <span class="org-tuareg-font-lock-operator">{</span> output_of_int $4 $6 $8 $2 <span class="org-tuareg-font-lock-operator">::</span> $1 <span class="org-tuareg-font-lock-operator">}</span>
<span class="org-tuareg-font-lock-operator">|</span> atoms_list <span class="org-tuareg-font-lock-constructor">INTEGER</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">EOL</span> <span class="org-tuareg-font-lock-operator">{</span> output_of_int $4 $6 $8 $2 <span class="org-tuareg-font-lock-operator">::</span> $1 <span class="org-tuareg-font-lock-operator">}</span>
<span class="org-tuareg-font-lock-operator">|</span> atoms_list <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">WORD</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">EOL</span> <span class="org-tuareg-font-lock-operator">{</span> output_of_string $5 $7 $9 $3 <span class="org-tuareg-font-lock-operator">::</span> $1 <span class="org-tuareg-font-lock-operator">}</span>
<span class="org-tuareg-font-lock-operator">|</span> atoms_list <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">WORD</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">EOL</span> <span class="org-tuareg-font-lock-operator">{</span> output_of_string $5 $7 $9 $3 <span class="org-tuareg-font-lock-operator">::</span> $1 <span class="org-tuareg-font-lock-operator">}</span>
<span class="org-tuareg-font-lock-operator">|</span> atoms_list <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">INTEGER</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">EOL</span> <span class="org-tuareg-font-lock-operator">{</span> output_of_int $5 $7 $9 $3 <span class="org-tuareg-font-lock-operator">::</span> $1 <span class="org-tuareg-font-lock-operator">}</span>
<span class="org-tuareg-font-lock-operator">|</span> atoms_list <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">INTEGER</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">FLOAT</span> <span class="org-tuareg-font-lock-constructor">SPACE</span> <span class="org-tuareg-font-lock-constructor">EOL</span> <span class="org-tuareg-font-lock-operator">{</span> output_of_int $5 $7 $9 $3 <span class="org-tuareg-font-lock-operator">::</span> $1 <span class="org-tuareg-font-lock-operator">}</span>
<span class="org-tuareg-font-lock-operator">;</span>
</pre>
</div>
<p>
When an xyz file is read by <code>xyz_parser.mly</code>, it is converted into
an <code>xyz_file</code> data structure.
</p>
<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>
<span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">nucleus</span> <span class="org-tuareg-font-lock-operator">=</span>
<span class="org-tuareg-font-lock-operator">{</span>
element<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>
coord <span class="org-tuareg-font-lock-operator">:</span> <span class="org-tuareg-font-lock-module">Coordinate.</span>angstrom <span class="org-tuareg-font-lock-module">Coordinate.</span>point<span class="org-tuareg-font-lock-operator">;</span>
<span class="org-tuareg-font-lock-operator">}</span>
<span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">xyz_file</span> <span class="org-tuareg-font-lock-operator">=</span>
<span class="org-tuareg-font-lock-operator">{</span>
number_of_atoms <span class="org-tuareg-font-lock-operator">:</span> int <span class="org-tuareg-font-lock-operator">;</span>
file_title <span class="org-tuareg-font-lock-operator">:</span> string <span class="org-tuareg-font-lock-operator">;</span>
nuclei <span class="org-tuareg-font-lock-operator">:</span> nucleus list <span class="org-tuareg-font-lock-operator">;</span>
<span class="org-tuareg-font-lock-operator">}</span>
</pre>
</div>
</div>
</div>
</div>
<div id="outline-container-orgfe57c35" class="outline-3">
<h3 id="orgfe57c35"><span class="section-number-3">5.3</span> Conversion</h3>
<div class="outline-text-3" id="text-5-3">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">of_xyz_string</span> <span class="org-tuareg-font-lock-operator">:</span> string <span class="org-tuareg-font-lock-operator">-&gt;</span> t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">to_xyz_string</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> string
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">of_xyz_file</span> <span class="org-tuareg-font-lock-operator">:</span> string <span class="org-tuareg-font-lock-operator">-&gt;</span> t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">of_zmt_string</span> <span class="org-tuareg-font-lock-operator">:</span> string <span class="org-tuareg-font-lock-operator">-&gt;</span> t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">of_zmt_file</span> <span class="org-tuareg-font-lock-operator">:</span> string <span class="org-tuareg-font-lock-operator">-&gt;</span> t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">to_string</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> string
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">of_filename</span> <span class="org-tuareg-font-lock-operator">:</span> string <span class="org-tuareg-font-lock-operator">-&gt;</span> t
</pre>
</div>
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
<col class="org-left" />
<col class="org-left" />
</colgroup>
<tbody>
<tr>
<td class="org-left"><code>of_xyz_string</code></td>
<td class="org-left">Create from a string, in xyz format</td>
</tr>
<tr>
<td class="org-left"><code>of_xyz_file</code></td>
<td class="org-left">Create from a file, in xyz format</td>
</tr>
<tr>
<td class="org-left"><code>of_zmt_string</code></td>
<td class="org-left">Create from a string, in z-matrix format</td>
</tr>
<tr>
<td class="org-left"><code>of_zmt_file</code></td>
<td class="org-left">Create from a file, in z-matrix format</td>
</tr>
<tr>
<td class="org-left"><code>to_string</code></td>
<td class="org-left">Transform to a string, for printing</td>
</tr>
<tr>
<td class="org-left"><code>of_filename</code></td>
<td class="org-left">Detects the type of file (xyz, z-matrix) and reads the file</td>
</tr>
</tbody>
</table>
</div>
</div>
<div id="outline-container-org14de381" class="outline-3">
<h3 id="org14de381"><span class="section-number-3">5.4</span> Query</h3>
<div class="outline-text-3" id="text-5-4">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">formula</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> string
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">repulsion</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> float
<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
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">small_core</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> int
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">large_core</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> int
</pre>
</div>
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
<col class="org-left" />
<col class="org-left" />
</colgroup>
<tbody>
<tr>
<td class="org-left"><code>formula</code></td>
<td class="org-left">Returns the chemical formula</td>
</tr>
<tr>
<td class="org-left"><code>repulsion</code></td>
<td class="org-left">Nuclear repulsion energy, in atomic units</td>
</tr>
<tr>
<td class="org-left"><code>charge</code></td>
<td class="org-left">Sum of the charges of the nuclei</td>
</tr>
<tr>
<td class="org-left"><code>small_core</code></td>
<td class="org-left">Number of core electrons in the small core model</td>
</tr>
<tr>
<td class="org-left"><code>large_core</code></td>
<td class="org-left">Number of core electrons in the large core model</td>
</tr>
</tbody>
</table>
</div>
</div>
<div id="outline-container-org9224cc6" class="outline-3">
<h3 id="org9224cc6"><span class="section-number-3">5.5</span> TREXIO</h3>
<div class="outline-text-3" id="text-5-5">
</div>
<div id="outline-container-org7046b2a" class="outline-4">
<h4 id="org7046b2a"><span class="section-number-4">5.5.1</span> Read</h4>
<div class="outline-text-4" id="text-5-5-1">
<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_trexio</span> <span class="org-tuareg-font-lock-operator">:</span> <span class="org-tuareg-font-lock-module">Trexio.</span>trexio_file <span class="org-tuareg-font-lock-operator">-&gt;</span> t
</pre>
</div>
</div>
</div>
<div id="outline-container-orgd1b3675" class="outline-4">
<h4 id="orgd1b3675"><span class="section-number-4">5.5.2</span> Write</h4>
<div class="outline-text-4" id="text-5-5-2">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">to_trexio</span> <span class="org-tuareg-font-lock-operator">:</span> <span class="org-tuareg-font-lock-module">Trexio.</span>trexio_file <span class="org-tuareg-font-lock-operator">-&gt;</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> unit
</pre>
</div>
</div>
</div>
</div>
<div id="outline-container-org3ece660" class="outline-3">
<h3 id="org3ece660"><span class="section-number-3">5.6</span> Printers</h3>
<div class="outline-text-3" id="text-5-6">
<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
</pre>
</div>
</div>
</div>
<div id="outline-container-org6a90479" class="outline-3">
<h3 id="org6a90479"><span class="section-number-3">5.7</span> Tests</h3>
</div>
</div>
<div id="outline-container-org46003da" class="outline-2">
<h2 id="org46003da"><span class="section-number-2">6</span> Z-matrix</h2>
<div class="outline-text-2" id="text-6">
<p>
Z-matrix representation of nuclear coordinates.
</p>
</div>
<div id="outline-container-org5fcb7ed" class="outline-3">
<h3 id="org5fcb7ed"><span class="section-number-3">6.1</span> Type</h3>
<div class="outline-text-3" id="text-6-1">
<div class="org-src-container">
<pre class="src src-ocaml" id="orgf9db5fa"><span class="org-tuareg-font-lock-governing">type</span> <span class="org-type">t</span>
</pre>
</div>
</div>
</div>
<div id="outline-container-orga6c6d0e" class="outline-3">
<h3 id="orga6c6d0e"><span class="section-number-3">6.2</span> Conversion</h3>
<div class="outline-text-3" id="text-6-2">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">of_string</span> <span class="org-tuareg-font-lock-operator">:</span> string <span class="org-tuareg-font-lock-operator">-&gt;</span> t
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">to_xyz</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-operator">(</span><span class="org-tuareg-font-lock-module">Element.</span>t <span class="org-tuareg-font-lock-operator">*</span> float <span class="org-tuareg-font-lock-operator">*</span> float <span class="org-tuareg-font-lock-operator">*</span> float<span class="org-tuareg-font-lock-operator">)</span> array
<span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">to_xyz_string</span> <span class="org-tuareg-font-lock-operator">:</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> string
</pre>
</div>
<table border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
<col class="org-left" />
<col class="org-left" />
</colgroup>
<tbody>
<tr>
<td class="org-left"><code>of_string</code></td>
<td class="org-left">Reads a z-matrix from a string</td>
</tr>
<tr>
<td class="org-left"><code>to_xyz</code></td>
<td class="org-left">Converts to xyz format, as in the <code>Nuclei</code> module</td>
</tr>
<tr>
<td class="org-left"><code>to_xyz_string</code></td>
<td class="org-left">Converts to xyz format, as a string</td>
</tr>
</tbody>
</table>
<pre class="example" id="org7e18520">
let zmt = Zmatrix.of_string "
n
n 1 nn
h 1 hn 2 hnn
h 2 hn 1 hnn 3 dih4
h 1 hn 2 hnn 4 dih5
h 2 hn 1 hnn 3 dih5
nn 1.446
hn 1.016
hnn 106.0
dih4 -54.38
dih5 54.38
" ;;
- : Zmatrix.t = N
N 1 1.446000
H 1 1.016000 2 106.000000
H 2 1.016000 1 106.000000 3 -54.380000
H 1 1.016000 2 106.000000 4 54.380000
H 2 1.016000 1 106.000000 3 54.380000
Zmatrix.to_xyz zmt ;;
- : (Element.t * float * float * float) array =
[|(N, 0., 0., 0.); (N, 0., 0., 1.446);
(H, -0.976641883073332107, 0., -0.280047553510071046);
(H, -0.568802835186988709, 0.793909757123734683, 1.726047553510071);
(H, 0.314092649983635563, 0.924756819385119, -0.280047553510071101);
(H, -0.568802835186988709, -0.793909757123734683, 1.726047553510071)|]
Zmatrix.to_xyz_string zmt ;;
- : string =
"N 0.000000 0.000000 0.000000
N 0.000000 0.000000 1.446000
H -0.976642 0.000000 -0.280048
H -0.568803 0.793910 1.726048
H 0.314093 0.924757 -0.280048
H -0.568803 -0.793910 1.726048"
</pre>
</div>
</div>
<div id="outline-container-org37a7c2e" class="outline-3">
<h3 id="org37a7c2e"><span class="section-number-3">6.3</span> Printers</h3>
<div class="outline-text-3" id="text-6-3">
<div class="org-src-container">
<pre class="src src-ocaml"><span class="org-tuareg-font-lock-governing">val</span> <span class="org-function-name">pp</span> <span class="org-tuareg-font-lock-operator">:</span> <span class="org-tuareg-font-lock-module">Format.</span>formatter <span class="org-tuareg-font-lock-operator">-&gt;</span> t <span class="org-tuareg-font-lock-operator">-&gt;</span> unit
</pre>
</div>
</div>
</div>
</div>
</div>
<div id="postamble" class="status">
<p class="author">Author: Anthony Scemama</p>
<p class="date">Created: 2023-04-24 Mon 18:07</p>
<p class="validation"><a href="https://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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