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README.html
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2021-10-25 Mon 11:40 -->
<!-- 2021-10-25 Mon 15:00 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title>
@ -343,7 +343,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2021-10-25 Mon 11:40</p>
<p class="date">Created: 2021-10-25 Mon 15:00</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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Sparse.html
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2021-10-25 Mon 11:40 -->
<!-- 2021-10-25 Mon 15:00 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>&lrm;</title>
@ -232,8 +232,8 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org20dedfd">1. Text back end</a></li>
<li><a href="#orge09deb8">2. HDF5 Back end</a></li>
<li><a href="#orgdbd98ed">1. Text back end</a></li>
<li><a href="#org54311b5">2. HDF5 Back end</a></li>
</ul>
</div>
</div>
@ -241,8 +241,8 @@ for the JavaScript code in this tag.
See templator<sub>front.org</sub>
</p>
<div id="outline-container-org20dedfd" class="outline-2">
<h2 id="org20dedfd"><span class="section-number-2">1</span> Text back end</h2>
<div id="outline-container-orgdbd98ed" class="outline-2">
<h2 id="orgdbd98ed"><span class="section-number-2">1</span> Text back end</h2>
<div class="outline-text-2" id="text-1">
<p>
As the size of the dataset should be extensible, the simplest
@ -256,8 +256,8 @@ The offset can be used with <code>fseek(69L*offset, SEEK_SET)</code>
</div>
</div>
<div id="outline-container-orge09deb8" class="outline-2">
<h2 id="orge09deb8"><span class="section-number-2">2</span> HDF5 Back end</h2>
<div id="outline-container-org54311b5" class="outline-2">
<h2 id="org54311b5"><span class="section-number-2">2</span> HDF5 Back end</h2>
<div class="outline-text-2" id="text-2">
<p>
We need to declare the number of rows of the dataset as
@ -278,7 +278,7 @@ If the offset+num &gt; nmax, we need to extend the dataset.
</div>
</div>
<div id="postamble" class="status">
<p class="date">Created: 2021-10-25 Mon 11:40</p>
<p class="date">Created: 2021-10-25 Mon 15:00</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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index.html
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2021-10-25 Mon 11:40 -->
<!-- 2021-10-25 Mon 15:00 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title>
@ -343,7 +343,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2021-10-25 Mon 11:40</p>
<p class="date">Created: 2021-10-25 Mon 15:00</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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templator_front.html
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2021-10-25 Mon 11:40 -->
<!-- 2021-10-25 Mon 15:00 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Front end API</title>
@ -333,125 +333,125 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org740c08e">1. Coding conventions</a>
<li><a href="#orgeef4be1">1. Coding conventions</a>
<ul>
<li><a href="#org0e93b95">1.1. Memory allocation</a></li>
<li><a href="#orgece0e73">1.1. Memory allocation</a></li>
</ul>
</li>
<li><a href="#org2cd22c7">2. Front end</a>
<li><a href="#org2dfaae3">2. Front end</a>
<ul>
<li><a href="#org1ee21b9">2.1. Error handling</a>
<li><a href="#orge8e0ff4">2.1. Error handling</a>
<ul>
<li><a href="#orgc79ff68">2.1.1. Decoding errors</a>
<li><a href="#org2bf9540">2.1.1. Decoding errors</a>
<ul>
<li><a href="#org8db56ae">2.1.1.1. C source code</a></li>
<li><a href="#org7907afc">2.1.1.2. Fortran interface</a></li>
<li><a href="#org5aa3819">2.1.1.3. Python interface</a></li>
<li><a href="#org9fb1b18">2.1.1.1. C source code</a></li>
<li><a href="#org01beb7a">2.1.1.2. Fortran interface</a></li>
<li><a href="#org663a286">2.1.1.3. Python interface</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org6c4c7b4">2.2. Back ends</a>
<li><a href="#orgec65dd8">2.2. Back ends</a>
<ul>
<li><a href="#org37cacc6">2.2.1. C</a></li>
<li><a href="#org19d4800">2.2.2. Fortran</a></li>
<li><a href="#org08069d4">2.2.3. Python</a></li>
<li><a href="#org7dd7aaa">2.2.1. C</a></li>
<li><a href="#org71252ff">2.2.2. Fortran</a></li>
<li><a href="#org971166f">2.2.3. Python</a></li>
</ul>
</li>
<li><a href="#org64f31a3">2.3. Read/write behavior</a></li>
<li><a href="#org647d64f">2.4. TREXIO file type</a>
<li><a href="#orgef48d43">2.3. Read/write behavior</a></li>
<li><a href="#orgba6fe76">2.4. TREXIO file type</a>
<ul>
<li><a href="#org1ccf595">2.4.1. TREXIO<sub>File</sub> Python class</a></li>
<li><a href="#org35fdb71">2.4.1. TREXIO<sub>File</sub> Python class</a></li>
</ul>
</li>
<li><a href="#org9e7d7d8">2.5. Polymorphism of the file handle</a></li>
<li><a href="#org6a83212">2.6. File opening</a>
<li><a href="#orge0681f9">2.5. Polymorphism of the file handle</a></li>
<li><a href="#org4a47849">2.6. File opening</a>
<ul>
<li><a href="#org93efadd">2.6.1. C</a></li>
<li><a href="#org867c729">2.6.2. Fortran</a></li>
<li><a href="#orgdbab59c">2.6.3. Python</a></li>
<li><a href="#org5278712">2.6.4. Zero-based versus one-based arrays of indices</a></li>
<li><a href="#orge1428dd">2.6.1. C</a></li>
<li><a href="#org3a7973f">2.6.2. Fortran</a></li>
<li><a href="#org06b4b82">2.6.3. Python</a></li>
<li><a href="#org7348eed">2.6.4. Zero-based versus one-based arrays of indices</a></li>
</ul>
</li>
<li><a href="#org6a3e271">2.7. File closing</a>
<li><a href="#orgdc32d94">2.7. File closing</a>
<ul>
<li><a href="#orgdc2af07">2.7.1. C</a></li>
<li><a href="#org4b7f352">2.7.2. Fortran</a></li>
<li><a href="#orgad6a674">2.7.3. Python</a></li>
<li><a href="#org9821133">2.7.1. C</a></li>
<li><a href="#org577acbb">2.7.2. Fortran</a></li>
<li><a href="#org97f6f08">2.7.3. Python</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org54b0114">3. Templates for front end</a>
<li><a href="#org212e0f5">3. Templates for front end</a>
<ul>
<li><a href="#org90b4ace">3.1. Description</a></li>
<li><a href="#org4ace052">3.2. Templates for front end has/read/write a single numerical attribute</a>
<li><a href="#orgdaf089f">3.1. Description</a></li>
<li><a href="#org4cc5c45">3.2. Templates for front end has/read/write a single numerical attribute</a>
<ul>
<li><a href="#orgb77bdbc">3.2.1. Introduction</a></li>
<li><a href="#org8ebd1ce">3.2.2. C templates for front end</a>
<li><a href="#org1b4b031">3.2.1. Introduction</a></li>
<li><a href="#org416ecec">3.2.2. C templates for front end</a>
<ul>
<li><a href="#orgaf5a457">3.2.2.1. Function declarations</a></li>
<li><a href="#org1a1bd5a">3.2.2.2. Source code for double precision functions</a></li>
<li><a href="#orgc3e68a3">3.2.2.3. Source code for single precision functions</a></li>
<li><a href="#org2363072">3.2.2.4. Source code for default functions</a></li>
<li><a href="#orgff73069">3.2.2.1. Function declarations</a></li>
<li><a href="#org6d69899">3.2.2.2. Source code for double precision functions</a></li>
<li><a href="#orgf3b12da">3.2.2.3. Source code for single precision functions</a></li>
<li><a href="#org69176f7">3.2.2.4. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#org58af722">3.2.3. Fortran templates for front end</a></li>
<li><a href="#orga2248e6">3.2.4. Python templates for front end</a></li>
<li><a href="#org059d4d4">3.2.3. Fortran templates for front end</a></li>
<li><a href="#org013a9e6">3.2.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#org152b0e9">3.3. Templates for front end has/read/write a dataset of numerical data</a>
<li><a href="#org14283ee">3.3. Templates for front end has/read/write a dataset of numerical data</a>
<ul>
<li><a href="#orgc7a4b18">3.3.1. Introduction</a></li>
<li><a href="#orgab1f18c">3.3.2. C templates for front end</a>
<li><a href="#org49343b8">3.3.1. Introduction</a></li>
<li><a href="#org1a15018">3.3.2. C templates for front end</a>
<ul>
<li><a href="#org5fb8edb">3.3.2.1. Function declarations</a></li>
<li><a href="#orgab9f7d5">3.3.2.2. Source code for double precision functions</a></li>
<li><a href="#org41781d1">3.3.2.3. Source code for single precision functions</a></li>
<li><a href="#org1feb54a">3.3.2.4. Source code for memory-safe functions</a></li>
<li><a href="#org6689e2b">3.3.2.5. Source code for default functions</a></li>
<li><a href="#orgb873c0f">3.3.2.1. Function declarations</a></li>
<li><a href="#orga6a26ce">3.3.2.2. Source code for double precision functions</a></li>
<li><a href="#orgb715b14">3.3.2.3. Source code for single precision functions</a></li>
<li><a href="#org8fb1eea">3.3.2.4. Source code for memory-safe functions</a></li>
<li><a href="#orge098eb6">3.3.2.5. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#org2c3ceac">3.3.3. Fortran templates for front end</a></li>
<li><a href="#org7c303d3">3.3.4. Python templates for front end</a></li>
<li><a href="#org5f5d295">3.3.3. Fortran templates for front end</a></li>
<li><a href="#org2cb99d3">3.3.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#org07ff2f0">3.4. Sparse data structures</a></li>
<li><a href="#orge48e012">3.5. Templates for front end has/read/write a dataset of strings</a>
<li><a href="#org57e6dbc">3.4. Sparse data structures</a></li>
<li><a href="#org2995ee0">3.5. Templates for front end has/read/write a dataset of strings</a>
<ul>
<li><a href="#org1c2a213">3.5.1. Introduction</a></li>
<li><a href="#org2b601ce">3.5.2. C templates for front end</a>
<li><a href="#orgbc94b29">3.5.1. Introduction</a></li>
<li><a href="#org6cca135">3.5.2. C templates for front end</a>
<ul>
<li><a href="#orga8fa748">3.5.2.1. Function declarations</a></li>
<li><a href="#org838650e">3.5.2.2. Source code for default functions</a></li>
<li><a href="#orgb50058f">3.5.2.1. Function declarations</a></li>
<li><a href="#org2728972">3.5.2.2. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#orga001761">3.5.3. Fortran templates for front end</a></li>
<li><a href="#org5edce40">3.5.4. Python templates for front end</a></li>
<li><a href="#org47aad61">3.5.3. Fortran templates for front end</a></li>
<li><a href="#org43d9ebc">3.5.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#orgda7ab41">3.6. Templates for front end has/read/write a single string attribute</a>
<li><a href="#org1e883cc">3.6. Templates for front end has/read/write a single string attribute</a>
<ul>
<li><a href="#org897b5cf">3.6.1. Introduction</a></li>
<li><a href="#org66d9878">3.6.2. C templates for front end</a>
<li><a href="#orgd6c8d78">3.6.1. Introduction</a></li>
<li><a href="#org6bef09c">3.6.2. C templates for front end</a>
<ul>
<li><a href="#orgb09a129">3.6.2.1. Function declarations</a></li>
<li><a href="#org27748b6">3.6.2.2. Source code for default functions</a></li>
<li><a href="#org970a5d0">3.6.2.1. Function declarations</a></li>
<li><a href="#org5353ef3">3.6.2.2. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#org77d1385">3.6.3. Fortran templates for front end</a></li>
<li><a href="#org0b50074">3.6.4. Python templates for front end</a></li>
<li><a href="#orgfe98e27">3.6.3. Fortran templates for front end</a></li>
<li><a href="#org64c378a">3.6.4. Python templates for front end</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgaeef187">4. Fortran helper/wrapper functions</a></li>
<li><a href="#org852a919">4. Fortran helper/wrapper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-org740c08e" class="outline-2">
<h2 id="org740c08e"><span class="section-number-2">1</span> Coding conventions</h2>
<div id="outline-container-orgeef4be1" class="outline-2">
<h2 id="orgeef4be1"><span class="section-number-2">1</span> Coding conventions</h2>
<div class="outline-text-2" id="text-1">
<ul class="org-ul">
<li>integer types will be defined using types given in <code>stdint.h</code></li>
@ -466,8 +466,8 @@ for the JavaScript code in this tag.
</ul>
</div>
<div id="outline-container-org0e93b95" class="outline-3">
<h3 id="org0e93b95"><span class="section-number-3">1.1</span> Memory allocation</h3>
<div id="outline-container-orgece0e73" class="outline-3">
<h3 id="orgece0e73"><span class="section-number-3">1.1</span> Memory allocation</h3>
<div class="outline-text-3" id="text-1-1">
<p>
Memory allocation of structures can be facilitated by using the
@ -502,8 +502,8 @@ The maximum string size for the filenames is 4096 characters.
</div>
</div>
<div id="outline-container-org2cd22c7" class="outline-2">
<h2 id="org2cd22c7"><span class="section-number-2">2</span> Front end</h2>
<div id="outline-container-org2dfaae3" class="outline-2">
<h2 id="org2dfaae3"><span class="section-number-2">2</span> Front end</h2>
<div class="outline-text-2" id="text-2">
<p>
All calls to TREXIO are thread-safe.
@ -511,10 +511,10 @@ TREXIO front end is modular, which simplifies implementation of new back ends.
</p>
</div>
<div id="outline-container-org1ee21b9" class="outline-3">
<h3 id="org1ee21b9"><span class="section-number-3">2.1</span> Error handling</h3>
<div id="outline-container-orge8e0ff4" class="outline-3">
<h3 id="orge8e0ff4"><span class="section-number-3">2.1</span> Error handling</h3>
<div class="outline-text-3" id="text-2-1">
<table id="org4a67da9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd39b1c0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -736,8 +736,8 @@ TREXIO front end is modular, which simplifies implementation of new back ends.
</div>
</div>
<div id="outline-container-orgc79ff68" class="outline-4">
<h4 id="orgc79ff68"><span class="section-number-4">2.1.1</span> Decoding errors</h4>
<div id="outline-container-org2bf9540" class="outline-4">
<h4 id="org2bf9540"><span class="section-number-4">2.1.1</span> Decoding errors</h4>
<div class="outline-text-4" id="text-2-1-1">
<p>
The <code>trexio_string_of_error</code> converts an exit code into a string. The
@ -760,8 +760,8 @@ The text strings are extracted from the previous table.
</p>
</div>
<div id="outline-container-org8db56ae" class="outline-5">
<h5 id="org8db56ae"><span class="section-number-5">2.1.1.1</span> C source code</h5>
<div id="outline-container-org9fb1b18" class="outline-5">
<h5 id="org9fb1b18"><span class="section-number-5">2.1.1.1</span> C source code</h5>
<div class="outline-text-5" id="text-2-1-1-1">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #a020f0;">const</span> <span style="color: #228b22;">char</span>*
@ -866,8 +866,8 @@ The text strings are extracted from the previous table.
</div>
</div>
<div id="outline-container-org7907afc" class="outline-5">
<h5 id="org7907afc"><span class="section-number-5">2.1.1.2</span> Fortran interface</h5>
<div id="outline-container-org01beb7a" class="outline-5">
<h5 id="org01beb7a"><span class="section-number-5">2.1.1.2</span> Fortran interface</h5>
<div class="outline-text-5" id="text-2-1-1-2">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">interface</span>
@ -883,8 +883,8 @@ The text strings are extracted from the previous table.
</div>
</div>
<div id="outline-container-org5aa3819" class="outline-5">
<h5 id="org5aa3819"><span class="section-number-5">2.1.1.3</span> Python interface</h5>
<div id="outline-container-org663a286" class="outline-5">
<h5 id="org663a286"><span class="section-number-5">2.1.1.3</span> Python interface</h5>
<div class="outline-text-5" id="text-2-1-1-3">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">class</span> <span style="color: #228b22;">Error</span>(<span style="color: #228b22;">Exception</span>):
@ -923,8 +923,8 @@ The text strings are extracted from the previous table.
</div>
</div>
<div id="outline-container-org6c4c7b4" class="outline-3">
<h3 id="org6c4c7b4"><span class="section-number-3">2.2</span> Back ends</h3>
<div id="outline-container-orgec65dd8" class="outline-3">
<h3 id="orgec65dd8"><span class="section-number-3">2.2</span> Back ends</h3>
<div class="outline-text-3" id="text-2-2">
<p>
TREXIO has several back ends:
@ -948,8 +948,8 @@ lines that correspond to the <code>TREXIO_JSON</code> back end (not implemented
</p>
</div>
<div id="outline-container-org37cacc6" class="outline-4">
<h4 id="org37cacc6"><span class="section-number-4">2.2.1</span> C</h4>
<div id="outline-container-org7dd7aaa" class="outline-4">
<h4 id="org7dd7aaa"><span class="section-number-4">2.2.1</span> C</h4>
<div class="outline-text-4" id="text-2-2-1">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #228b22;">int32_t</span> <span style="color: #228b22;">back_end_t</span>;
@ -965,8 +965,8 @@ lines that correspond to the <code>TREXIO_JSON</code> back end (not implemented
</div>
</div>
<div id="outline-container-org19d4800" class="outline-4">
<h4 id="org19d4800"><span class="section-number-4">2.2.2</span> Fortran</h4>
<div id="outline-container-org71252ff" class="outline-4">
<h4 id="org71252ff"><span class="section-number-4">2.2.2</span> Fortran</h4>
<div class="outline-text-4" id="text-2-2-2">
<div class="org-src-container">
<pre class="src src-f90"> <span style="color: #228b22;">integer</span>(trexio_backend), <span style="color: #a020f0;">parameter</span> ::<span style="color: #a0522d;"> TREXIO_HDF5 = 0</span>
@ -978,8 +978,8 @@ lines that correspond to the <code>TREXIO_JSON</code> back end (not implemented
</div>
</div>
<div id="outline-container-org08069d4" class="outline-4">
<h4 id="org08069d4"><span class="section-number-4">2.2.3</span> Python</h4>
<div id="outline-container-org971166f" class="outline-4">
<h4 id="org971166f"><span class="section-number-4">2.2.3</span> Python</h4>
<div class="outline-text-4" id="text-2-2-3">
<div class="org-src-container">
<pre class="src src-python"># <span style="color: #b22222;">define TREXIO back ends</span>
@ -993,8 +993,8 @@ lines that correspond to the <code>TREXIO_JSON</code> back end (not implemented
</div>
</div>
<div id="outline-container-org64f31a3" class="outline-3">
<h3 id="org64f31a3"><span class="section-number-3">2.3</span> Read/write behavior</h3>
<div id="outline-container-orgef48d43" class="outline-3">
<h3 id="orgef48d43"><span class="section-number-3">2.3</span> Read/write behavior</h3>
<div class="outline-text-3" id="text-2-3">
<p>
Every time a reading function is called, the data is read from the
@ -1022,8 +1022,8 @@ concurrent programs, the behavior is not specified.
</p>
</div>
</div>
<div id="outline-container-org647d64f" class="outline-3">
<h3 id="org647d64f"><span class="section-number-3">2.4</span> TREXIO file type</h3>
<div id="outline-container-orgba6fe76" class="outline-3">
<h3 id="orgba6fe76"><span class="section-number-3">2.4</span> TREXIO file type</h3>
<div class="outline-text-3" id="text-2-4">
<p>
<code>trexio_s</code> is the the main type for TREXIO files, visible to the users
@ -1057,8 +1057,8 @@ TREXIO files will have as a first argument the TREXIO file handle.
</div>
</div>
<div id="outline-container-org1ccf595" class="outline-4">
<h4 id="org1ccf595"><span class="section-number-4">2.4.1</span> TREXIO<sub>File</sub> Python class</h4>
<div id="outline-container-org35fdb71" class="outline-4">
<h4 id="org35fdb71"><span class="section-number-4">2.4.1</span> TREXIO<sub>File</sub> Python class</h4>
<div class="outline-text-4" id="text-2-4-1">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">class</span> <span style="color: #228b22;">File</span>:
@ -1131,8 +1131,8 @@ TREXIO files will have as a first argument the TREXIO file handle.
</div>
</div>
<div id="outline-container-org9e7d7d8" class="outline-3">
<h3 id="org9e7d7d8"><span class="section-number-3">2.5</span> Polymorphism of the file handle</h3>
<div id="outline-container-orge0681f9" class="outline-3">
<h3 id="orge0681f9"><span class="section-number-3">2.5</span> Polymorphism of the file handle</h3>
<div class="outline-text-3" id="text-2-5">
<p>
Polymorphism of the <code>trexio_t</code> type is handled by ensuring that the
@ -1151,8 +1151,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org6a83212" class="outline-3">
<h3 id="org6a83212"><span class="section-number-3">2.6</span> File opening</h3>
<div id="outline-container-org4a47849" class="outline-3">
<h3 id="org4a47849"><span class="section-number-3">2.6</span> File opening</h3>
<div class="outline-text-3" id="text-2-6">
<p>
<code>trexio_open</code> creates a new TREXIO file or opens existing one.
@ -1191,8 +1191,8 @@ renaming the <code>.txt</code> data files.
</p>
</div>
<div id="outline-container-org93efadd" class="outline-4">
<h4 id="org93efadd"><span class="section-number-4">2.6.1</span> C</h4>
<div id="outline-container-orge1428dd" class="outline-4">
<h4 id="orge1428dd"><span class="section-number-4">2.6.1</span> C</h4>
<div class="outline-text-4" id="text-2-6-1">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_t</span>*
@ -1359,8 +1359,8 @@ renaming the <code>.txt</code> data files.
</div>
</div>
<div id="outline-container-org867c729" class="outline-4">
<h4 id="org867c729"><span class="section-number-4">2.6.2</span> Fortran</h4>
<div id="outline-container-org3a7973f" class="outline-4">
<h4 id="org3a7973f"><span class="section-number-4">2.6.2</span> Fortran</h4>
<div class="outline-text-4" id="text-2-6-2">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">interface</span>
@ -1378,8 +1378,8 @@ renaming the <code>.txt</code> data files.
</div>
</div>
<div id="outline-container-orgdbab59c" class="outline-4">
<h4 id="orgdbab59c"><span class="section-number-4">2.6.3</span> Python</h4>
<div id="outline-container-org06b4b82" class="outline-4">
<h4 id="org06b4b82"><span class="section-number-4">2.6.3</span> Python</h4>
<div class="outline-text-4" id="text-2-6-3">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">def</span> <span style="color: #0000ff;">open</span>(file_name: <span style="color: #483d8b;">str</span>, mode: <span style="color: #483d8b;">str</span>, back_end: <span style="color: #483d8b;">int</span>):
@ -1427,8 +1427,8 @@ renaming the <code>.txt</code> data files.
</div>
</div>
<div id="outline-container-org5278712" class="outline-4">
<h4 id="org5278712"><span class="section-number-4">2.6.4</span> Zero-based versus one-based arrays of indices</h4>
<div id="outline-container-org7348eed" class="outline-4">
<h4 id="org7348eed"><span class="section-number-4">2.6.4</span> Zero-based versus one-based arrays of indices</h4>
<div class="outline-text-4" id="text-2-6-4">
<p>
Because arrays are zero-based in Fortran, we need to set a flag to
@ -1461,8 +1461,8 @@ know if we need to shift by 1 arrays of indices.
</div>
</div>
<div id="outline-container-org6a3e271" class="outline-3">
<h3 id="org6a3e271"><span class="section-number-3">2.7</span> File closing</h3>
<div id="outline-container-orgdc32d94" class="outline-3">
<h3 id="orgdc32d94"><span class="section-number-3">2.7</span> File closing</h3>
<div class="outline-text-3" id="text-2-7">
<p>
<code>trexio_close</code> closes an existing <code>trexio_t</code> file.
@ -1479,8 +1479,8 @@ output:
</p>
</div>
<div id="outline-container-orgdc2af07" class="outline-4">
<h4 id="orgdc2af07"><span class="section-number-4">2.7.1</span> C</h4>
<div id="outline-container-org9821133" class="outline-4">
<h4 id="org9821133"><span class="section-number-4">2.7.1</span> C</h4>
<div class="outline-text-4" id="text-2-7-1">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1551,8 +1551,8 @@ output:
</div>
</div>
<div id="outline-container-org4b7f352" class="outline-4">
<h4 id="org4b7f352"><span class="section-number-4">2.7.2</span> Fortran</h4>
<div id="outline-container-org577acbb" class="outline-4">
<h4 id="org577acbb"><span class="section-number-4">2.7.2</span> Fortran</h4>
<div class="outline-text-4" id="text-2-7-2">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">interface</span>
@ -1566,8 +1566,8 @@ output:
</div>
</div>
<div id="outline-container-orgad6a674" class="outline-4">
<h4 id="orgad6a674"><span class="section-number-4">2.7.3</span> Python</h4>
<div id="outline-container-org97f6f08" class="outline-4">
<h4 id="org97f6f08"><span class="section-number-4">2.7.3</span> Python</h4>
<div class="outline-text-4" id="text-2-7-3">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">def</span> <span style="color: #0000ff;">close</span>(trexio_file):
@ -1589,12 +1589,12 @@ output:
</div>
</div>
<div id="outline-container-org54b0114" class="outline-2">
<h2 id="org54b0114"><span class="section-number-2">3</span> Templates for front end</h2>
<div id="outline-container-org212e0f5" class="outline-2">
<h2 id="org212e0f5"><span class="section-number-2">3</span> Templates for front end</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org90b4ace" class="outline-3">
<h3 id="org90b4ace"><span class="section-number-3">3.1</span> Description</h3>
<div id="outline-container-orgdaf089f" class="outline-3">
<h3 id="orgdaf089f"><span class="section-number-3">3.1</span> Description</h3>
<div class="outline-text-3" id="text-3-1">
<p>
Consider the following block of <code>trex.json</code>:
@ -1815,12 +1815,12 @@ value will result in <code>TREXIO_INVALID_ARG_2</code> exit code.
</div>
</div>
<div id="outline-container-org4ace052" class="outline-3">
<h3 id="org4ace052"><span class="section-number-3">3.2</span> Templates for front end has/read/write a single numerical attribute</h3>
<div id="outline-container-org4cc5c45" class="outline-3">
<h3 id="org4cc5c45"><span class="section-number-3">3.2</span> Templates for front end has/read/write a single numerical attribute</h3>
<div class="outline-text-3" id="text-3-2">
</div>
<div id="outline-container-orgb77bdbc" class="outline-4">
<h4 id="orgb77bdbc"><span class="section-number-4">3.2.1</span> Introduction</h4>
<div id="outline-container-org1b4b031" class="outline-4">
<h4 id="org1b4b031"><span class="section-number-4">3.2.1</span> Introduction</h4>
<div class="outline-text-4" id="text-3-2-1">
<p>
This section concerns API calls related to numerical attributes,
@ -1891,8 +1891,8 @@ namely single value of int/float types.
</div>
</div>
<div id="outline-container-org8ebd1ce" class="outline-4">
<h4 id="org8ebd1ce"><span class="section-number-4">3.2.2</span> C templates for front end</h4>
<div id="outline-container-org416ecec" class="outline-4">
<h4 id="org416ecec"><span class="section-number-4">3.2.2</span> C templates for front end</h4>
<div class="outline-text-4" id="text-3-2-2">
<p>
The <code>C</code> templates that correspond to each of the abovementioned
@ -1906,12 +1906,12 @@ precision (see Table above).
</p>
</div>
<div id="outline-container-orgaf5a457" class="outline-5">
<h5 id="orgaf5a457"><span class="section-number-5">3.2.2.1</span> Function declarations</h5>
<div id="outline-container-orgff73069" class="outline-5">
<h5 id="orgff73069"><span class="section-number-5">3.2.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-org1a1bd5a" class="outline-5">
<h5 id="org1a1bd5a"><span class="section-number-5">3.2.2.2</span> Source code for double precision functions</h5>
<div id="outline-container-org6d69899" class="outline-5">
<h5 id="org6d69899"><span class="section-number-5">3.2.2.2</span> Source code for double precision functions</h5>
<div class="outline-text-5" id="text-3-2-2-2">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1972,8 +1972,8 @@ precision (see Table above).
</div>
</div>
<div id="outline-container-orgc3e68a3" class="outline-5">
<h5 id="orgc3e68a3"><span class="section-number-5">3.2.2.3</span> Source code for single precision functions</h5>
<div id="outline-container-orgf3b12da" class="outline-5">
<h5 id="orgf3b12da"><span class="section-number-5">3.2.2.3</span> Source code for single precision functions</h5>
<div class="outline-text-5" id="text-3-2-2-3">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -2041,8 +2041,8 @@ precision (see Table above).
</div>
</div>
<div id="outline-container-org2363072" class="outline-5">
<h5 id="org2363072"><span class="section-number-5">3.2.2.4</span> Source code for default functions</h5>
<div id="outline-container-org69176f7" class="outline-5">
<h5 id="org69176f7"><span class="section-number-5">3.2.2.4</span> Source code for default functions</h5>
<div class="outline-text-5" id="text-3-2-2-4">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -2095,8 +2095,8 @@ precision (see Table above).
</div>
</div>
<div id="outline-container-org58af722" class="outline-4">
<h4 id="org58af722"><span class="section-number-4">3.2.3</span> Fortran templates for front end</h4>
<div id="outline-container-org059d4d4" class="outline-4">
<h4 id="org059d4d4"><span class="section-number-4">3.2.3</span> Fortran templates for front end</h4>
<div class="outline-text-4" id="text-3-2-3">
<p>
The <code>Fortran</code> templates that provide an access to the <code>C</code> API calls from Fortran.
@ -2181,8 +2181,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-orga2248e6" class="outline-4">
<h4 id="orga2248e6"><span class="section-number-4">3.2.4</span> Python templates for front end</h4>
<div id="outline-container-org013a9e6" class="outline-4">
<h4 id="org013a9e6"><span class="section-number-4">3.2.4</span> Python templates for front end</h4>
<div class="outline-text-4" id="text-3-2-4">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">def</span> <span style="color: #0000ff;">write_</span>$group_num$(trexio_file, num_w: $group_num_py_dtype$) -&gt; <span style="color: #008b8b;">None</span>:
@ -2267,12 +2267,12 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-org152b0e9" class="outline-3">
<h3 id="org152b0e9"><span class="section-number-3">3.3</span> Templates for front end has/read/write a dataset of numerical data</h3>
<div id="outline-container-org14283ee" class="outline-3">
<h3 id="org14283ee"><span class="section-number-3">3.3</span> Templates for front end has/read/write a dataset of numerical data</h3>
<div class="outline-text-3" id="text-3-3">
</div>
<div id="outline-container-orgc7a4b18" class="outline-4">
<h4 id="orgc7a4b18"><span class="section-number-4">3.3.1</span> Introduction</h4>
<div id="outline-container-org49343b8" class="outline-4">
<h4 id="org49343b8"><span class="section-number-4">3.3.1</span> Introduction</h4>
<div class="outline-text-4" id="text-3-3-1">
<p>
This section concerns API calls related to datasets.
@ -2354,8 +2354,8 @@ This section concerns API calls related to datasets.
</div>
</div>
<div id="outline-container-orgab1f18c" class="outline-4">
<h4 id="orgab1f18c"><span class="section-number-4">3.3.2</span> C templates for front end</h4>
<div id="outline-container-org1a15018" class="outline-4">
<h4 id="org1a15018"><span class="section-number-4">3.3.2</span> C templates for front end</h4>
<div class="outline-text-4" id="text-3-3-2">
<p>
The C templates that correspond to each of the abovementioned functions can be found below.
@ -2366,13 +2366,13 @@ The basic (non-suffixed) API call on datasets deals with double precision (see T
</p>
</div>
<div id="outline-container-org5fb8edb" class="outline-5">
<h5 id="org5fb8edb"><span class="section-number-5">3.3.2.1</span> Function declarations</h5>
<div id="outline-container-orgb873c0f" class="outline-5">
<h5 id="orgb873c0f"><span class="section-number-5">3.3.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-orgab9f7d5" class="outline-5">
<h5 id="orgab9f7d5"><span class="section-number-5">3.3.2.2</span> Source code for double precision functions</h5>
<div id="outline-container-orga6a26ce" class="outline-5">
<h5 id="orga6a26ce"><span class="section-number-5">3.3.2.2</span> Source code for double precision functions</h5>
<div class="outline-text-5" id="text-3-3-2-2">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -2500,8 +2500,8 @@ The basic (non-suffixed) API call on datasets deals with double precision (see T
</div>
</div>
<div id="outline-container-org41781d1" class="outline-5">
<h5 id="org41781d1"><span class="section-number-5">3.3.2.3</span> Source code for single precision functions</h5>
<div id="outline-container-orgb715b14" class="outline-5">
<h5 id="orgb715b14"><span class="section-number-5">3.3.2.3</span> Source code for single precision functions</h5>
<div class="outline-text-5" id="text-3-3-2-3">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -2642,11 +2642,11 @@ The basic (non-suffixed) API call on datasets deals with double precision (see T
</div>
</div>
<div id="outline-container-org1feb54a" class="outline-5">
<h5 id="org1feb54a"><span class="section-number-5">3.3.2.4</span> Source code for memory-safe functions</h5>
<div id="outline-container-org8fb1eea" class="outline-5">
<h5 id="org8fb1eea"><span class="section-number-5">3.3.2.4</span> Source code for memory-safe functions</h5>
<div class="outline-text-5" id="text-3-3-2-4">
<div class="org-src-container">
<pre class="src src-c" id="org9d170d3"><span style="color: #228b22;">trexio_exit_code</span> <span style="color: #a0522d;">rc</span>;
<pre class="src src-c" id="org80bb45e"><span style="color: #228b22;">trexio_exit_code</span> <span style="color: #a0522d;">rc</span>;
int64_t $group_dset_dim$ = 0;
/* <span style="color: #b22222;">Error handling for this call is added by the generator </span>*/
@ -2802,8 +2802,8 @@ rc = trexio_read_$group_dset_dim$_64(file, &amp;($group_dset_dim$));
</div>
</div>
<div id="outline-container-org6689e2b" class="outline-5">
<h5 id="org6689e2b"><span class="section-number-5">3.3.2.5</span> Source code for default functions</h5>
<div id="outline-container-orge098eb6" class="outline-5">
<h5 id="orge098eb6"><span class="section-number-5">3.3.2.5</span> Source code for default functions</h5>
<div class="outline-text-5" id="text-3-3-2-5">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -2877,8 +2877,8 @@ rc = trexio_read_$group_dset_dim$_64(file, &amp;($group_dset_dim$));
</div>
</div>
<div id="outline-container-org2c3ceac" class="outline-4">
<h4 id="org2c3ceac"><span class="section-number-4">3.3.3</span> Fortran templates for front end</h4>
<div id="outline-container-org5f5d295" class="outline-4">
<h4 id="org5f5d295"><span class="section-number-4">3.3.3</span> Fortran templates for front end</h4>
<div class="outline-text-4" id="text-3-3-3">
<p>
The <code>Fortran</code> templates that provide an access to the <code>C</code> API calls from <code>Fortran</code>.
@ -2963,8 +2963,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-org7c303d3" class="outline-4">
<h4 id="org7c303d3"><span class="section-number-4">3.3.4</span> Python templates for front end</h4>
<div id="outline-container-org2cb99d3" class="outline-4">
<h4 id="org2cb99d3"><span class="section-number-4">3.3.4</span> Python templates for front end</h4>
<div class="outline-text-4" id="text-3-3-4">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">def</span> <span style="color: #0000ff;">write_</span>$group_dset$(trexio_file, dset_w) -&gt; <span style="color: #008b8b;">None</span>:
@ -3159,8 +3159,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-org07ff2f0" class="outline-3">
<h3 id="org07ff2f0"><span class="section-number-3">3.4</span> Sparse data structures</h3>
<div id="outline-container-org57e6dbc" class="outline-3">
<h3 id="org57e6dbc"><span class="section-number-3">3.4</span> Sparse data structures</h3>
<div class="outline-text-3" id="text-3-4">
<p>
Sparse data structures are used typically for large tensors such as
@ -3301,12 +3301,12 @@ For the values,
</div>
</div>
<div id="outline-container-orge48e012" class="outline-3">
<h3 id="orge48e012"><span class="section-number-3">3.5</span> Templates for front end has/read/write a dataset of strings</h3>
<div id="outline-container-org2995ee0" class="outline-3">
<h3 id="org2995ee0"><span class="section-number-3">3.5</span> Templates for front end has/read/write a dataset of strings</h3>
<div class="outline-text-3" id="text-3-5">
</div>
<div id="outline-container-org1c2a213" class="outline-4">
<h4 id="org1c2a213"><span class="section-number-4">3.5.1</span> Introduction</h4>
<div id="outline-container-orgbc94b29" class="outline-4">
<h4 id="orgbc94b29"><span class="section-number-4">3.5.1</span> Introduction</h4>
<div class="outline-text-4" id="text-3-5-1">
<p>
This section concerns API calls related to datasets of strings.
@ -3346,8 +3346,8 @@ This section concerns API calls related to datasets of strings.
</div>
</div>
<div id="outline-container-org2b601ce" class="outline-4">
<h4 id="org2b601ce"><span class="section-number-4">3.5.2</span> C templates for front end</h4>
<div id="outline-container-org6cca135" class="outline-4">
<h4 id="org6cca135"><span class="section-number-4">3.5.2</span> C templates for front end</h4>
<div class="outline-text-4" id="text-3-5-2">
<p>
First parameter is the <code>TREXIO</code> file handle. Second parameter is the variable to be written/read
@ -3355,12 +3355,12 @@ to/from the <code>TREXIO</code> file (except for <code>trexio_has_</code> functi
</p>
</div>
<div id="outline-container-orga8fa748" class="outline-5">
<h5 id="orga8fa748"><span class="section-number-5">3.5.2.1</span> Function declarations</h5>
<div id="outline-container-orgb50058f" class="outline-5">
<h5 id="orgb50058f"><span class="section-number-5">3.5.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-org838650e" class="outline-5">
<h5 id="org838650e"><span class="section-number-5">3.5.2.2</span> Source code for default functions</h5>
<div id="outline-container-org2728972" class="outline-5">
<h5 id="org2728972"><span class="section-number-5">3.5.2.2</span> Source code for default functions</h5>
<div class="outline-text-5" id="text-3-5-2-2">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -3602,8 +3602,8 @@ to/from the <code>TREXIO</code> file (except for <code>trexio_has_</code> functi
</div>
</div>
<div id="outline-container-orga001761" class="outline-4">
<h4 id="orga001761"><span class="section-number-4">3.5.3</span> Fortran templates for front end</h4>
<div id="outline-container-org47aad61" class="outline-4">
<h4 id="org47aad61"><span class="section-number-4">3.5.3</span> Fortran templates for front end</h4>
<div class="outline-text-4" id="text-3-5-3">
<p>
The <code>Fortran</code> templates that provide an access to the <code>C</code> API calls from <code>Fortran</code>.
@ -3699,8 +3699,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-org5edce40" class="outline-4">
<h4 id="org5edce40"><span class="section-number-4">3.5.4</span> Python templates for front end</h4>
<div id="outline-container-org43d9ebc" class="outline-4">
<h4 id="org43d9ebc"><span class="section-number-4">3.5.4</span> Python templates for front end</h4>
<div class="outline-text-4" id="text-3-5-4">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">def</span> <span style="color: #0000ff;">write_</span>$group_dset$(trexio_file, dset_w: <span style="color: #483d8b;">list</span>) -&gt; <span style="color: #008b8b;">None</span>:
@ -3816,12 +3816,12 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-orgda7ab41" class="outline-3">
<h3 id="orgda7ab41"><span class="section-number-3">3.6</span> Templates for front end has/read/write a single string attribute</h3>
<div id="outline-container-org1e883cc" class="outline-3">
<h3 id="org1e883cc"><span class="section-number-3">3.6</span> Templates for front end has/read/write a single string attribute</h3>
<div class="outline-text-3" id="text-3-6">
</div>
<div id="outline-container-org897b5cf" class="outline-4">
<h4 id="org897b5cf"><span class="section-number-4">3.6.1</span> Introduction</h4>
<div id="outline-container-orgd6c8d78" class="outline-4">
<h4 id="orgd6c8d78"><span class="section-number-4">3.6.1</span> Introduction</h4>
<div class="outline-text-4" id="text-3-6-1">
<p>
This section concerns API calls related to string attributes.
@ -3861,16 +3861,16 @@ This section concerns API calls related to string attributes.
</div>
</div>
<div id="outline-container-org66d9878" class="outline-4">
<h4 id="org66d9878"><span class="section-number-4">3.6.2</span> C templates for front end</h4>
<div id="outline-container-org6bef09c" class="outline-4">
<h4 id="org6bef09c"><span class="section-number-4">3.6.2</span> C templates for front end</h4>
<div class="outline-text-4" id="text-3-6-2">
</div>
<div id="outline-container-orgb09a129" class="outline-5">
<h5 id="orgb09a129"><span class="section-number-5">3.6.2.1</span> Function declarations</h5>
<div id="outline-container-org970a5d0" class="outline-5">
<h5 id="org970a5d0"><span class="section-number-5">3.6.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-org27748b6" class="outline-5">
<h5 id="org27748b6"><span class="section-number-5">3.6.2.2</span> Source code for default functions</h5>
<div id="outline-container-org5353ef3" class="outline-5">
<h5 id="org5353ef3"><span class="section-number-5">3.6.2.2</span> Source code for default functions</h5>
<div class="outline-text-5" id="text-3-6-2-2">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -3970,8 +3970,8 @@ This section concerns API calls related to string attributes.
</div>
</div>
<div id="outline-container-org77d1385" class="outline-4">
<h4 id="org77d1385"><span class="section-number-4">3.6.3</span> Fortran templates for front end</h4>
<div id="outline-container-orgfe98e27" class="outline-4">
<h4 id="orgfe98e27"><span class="section-number-4">3.6.3</span> Fortran templates for front end</h4>
<div class="outline-text-4" id="text-3-6-3">
<p>
The <code>Fortran</code> templates that provide an access to the <code>C</code> API calls from Fortran.
@ -4048,8 +4048,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-org0b50074" class="outline-4">
<h4 id="org0b50074"><span class="section-number-4">3.6.4</span> Python templates for front end</h4>
<div id="outline-container-org64c378a" class="outline-4">
<h4 id="org64c378a"><span class="section-number-4">3.6.4</span> Python templates for front end</h4>
<div class="outline-text-4" id="text-3-6-4">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">def</span> <span style="color: #0000ff;">write_</span>$group_str$(trexio_file, str_w: <span style="color: #483d8b;">str</span>) -&gt; <span style="color: #008b8b;">None</span>:
@ -4139,8 +4139,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-orgaeef187" class="outline-2">
<h2 id="orgaeef187"><span class="section-number-2">4</span> Fortran helper/wrapper functions</h2>
<div id="outline-container-org852a919" class="outline-2">
<h2 id="org852a919"><span class="section-number-2">4</span> Fortran helper/wrapper functions</h2>
<div class="outline-text-2" id="text-4">
<p>
The function below adapts the original C-based <code>trexio_open</code> for Fortran.
@ -4275,7 +4275,7 @@ two code are identical, i.e. if the <code>assert</code> statement pass.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2021-10-25 Mon 11:40</p>
<p class="date">Created: 2021-10-25 Mon 15:00</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

52
templator_hdf5.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>
<!-- 2021-10-25 Mon 11:40 -->
<!-- 2021-10-25 Mon 15:00 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>HDF5 back end</title>
@ -311,27 +311,27 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org6325b54">1. HDF5 back end</a>
<li><a href="#org625e697">1. HDF5 back end</a>
<ul>
<li><a href="#org9b38088">1.1. Template for HDF5 definitions</a></li>
<li><a href="#org9682be7">1.2. Template for HDF5 structures</a></li>
<li><a href="#org9f5c9d8">1.3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgf23eee7">1.4. Template for HDF5 has/read/write the numerical attribute</a></li>
<li><a href="#org052cdfb">1.5. Template for HDF5 has/read/write the dataset of numerical data</a></li>
<li><a href="#orgea82545">1.6. Template for HDF5 has/read/write the dataset of strings</a></li>
<li><a href="#orgcc4451d">1.7. Template for HDF5 has/read/write the string attribute</a></li>
<li><a href="#org9433e90">1.1. Template for HDF5 definitions</a></li>
<li><a href="#orge1fc59e">1.2. Template for HDF5 structures</a></li>
<li><a href="#org89112ab">1.3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgd89e3c2">1.4. Template for HDF5 has/read/write the numerical attribute</a></li>
<li><a href="#org7bde5ad">1.5. Template for HDF5 has/read/write the dataset of numerical data</a></li>
<li><a href="#orgdef4bc9">1.6. Template for HDF5 has/read/write the dataset of strings</a></li>
<li><a href="#org1081ffb">1.7. Template for HDF5 has/read/write the string attribute</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org6325b54" class="outline-2">
<h2 id="org6325b54"><span class="section-number-2">1</span> HDF5 back end</h2>
<div id="outline-container-org625e697" class="outline-2">
<h2 id="org625e697"><span class="section-number-2">1</span> HDF5 back end</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-org9b38088" class="outline-3">
<h3 id="org9b38088"><span class="section-number-3">1.1</span> Template for HDF5 definitions</h3>
<div id="outline-container-org9433e90" class="outline-3">
<h3 id="org9433e90"><span class="section-number-3">1.1</span> Template for HDF5 definitions</h3>
<div class="outline-text-3" id="text-1-1">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #483d8b;">#define</span> $GROUP$_GROUP_NAME <span style="color: #8b2252;">"$group$"</span>
@ -343,8 +343,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org9682be7" class="outline-3">
<h3 id="org9682be7"><span class="section-number-3">1.2</span> Template for HDF5 structures</h3>
<div id="outline-container-orge1fc59e" class="outline-3">
<h3 id="orge1fc59e"><span class="section-number-3">1.2</span> Template for HDF5 structures</h3>
<div class="outline-text-3" id="text-1-2">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> <span style="color: #228b22;">trexio_hdf5_s</span> {
@ -358,8 +358,8 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-org9f5c9d8" class="outline-3">
<h3 id="org9f5c9d8"><span class="section-number-3">1.3</span> Template for HDF5 init/deinit</h3>
<div id="outline-container-org89112ab" class="outline-3">
<h3 id="org89112ab"><span class="section-number-3">1.3</span> Template for HDF5 init/deinit</h3>
<div class="outline-text-3" id="text-1-3">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -439,8 +439,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-orgf23eee7" class="outline-3">
<h3 id="orgf23eee7"><span class="section-number-3">1.4</span> Template for HDF5 has/read/write the numerical attribute</h3>
<div id="outline-container-orgd89e3c2" class="outline-3">
<h3 id="orgd89e3c2"><span class="section-number-3">1.4</span> Template for HDF5 has/read/write the numerical attribute</h3>
<div class="outline-text-3" id="text-1-4">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -534,8 +534,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org052cdfb" class="outline-3">
<h3 id="org052cdfb"><span class="section-number-3">1.5</span> Template for HDF5 has/read/write the dataset of numerical data</h3>
<div id="outline-container-org7bde5ad" class="outline-3">
<h3 id="org7bde5ad"><span class="section-number-3">1.5</span> Template for HDF5 has/read/write the dataset of numerical data</h3>
<div class="outline-text-3" id="text-1-5">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -658,8 +658,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-orgea82545" class="outline-3">
<h3 id="orgea82545"><span class="section-number-3">1.6</span> Template for HDF5 has/read/write the dataset of strings</h3>
<div id="outline-container-orgdef4bc9" class="outline-3">
<h3 id="orgdef4bc9"><span class="section-number-3">1.6</span> Template for HDF5 has/read/write the dataset of strings</h3>
<div class="outline-text-3" id="text-1-6">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -864,8 +864,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-orgcc4451d" class="outline-3">
<h3 id="orgcc4451d"><span class="section-number-3">1.7</span> Template for HDF5 has/read/write the string attribute</h3>
<div id="outline-container-org1081ffb" class="outline-3">
<h3 id="org1081ffb"><span class="section-number-3">1.7</span> Template for HDF5 has/read/write the string attribute</h3>
<div class="outline-text-3" id="text-1-7">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -992,7 +992,7 @@ for the JavaScript code in this tag.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2021-10-25 Mon 11:40</p>
<p class="date">Created: 2021-10-25 Mon 15:00</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

112
templator_text.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>
<!-- 2021-10-25 Mon 11:40 -->
<!-- 2021-10-25 Mon 15:00 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TEXT back end</title>
@ -311,26 +311,26 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org648530d">1. TEXT back end</a>
<li><a href="#orgaa7d394">1. TEXT back end</a>
<ul>
<li><a href="#org5e031d6">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#org7abf142">1.2. Template for general structure in text back end</a></li>
<li><a href="#org4586757">1.3. Initialize function (constant part)</a></li>
<li><a href="#orgec78b04">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#org240b0c4">1.5. Template for text read struct</a></li>
<li><a href="#orgabab9a1">1.6. Template for text flush struct</a></li>
<li><a href="#org7e12d9b">1.7. Template for text free memory</a></li>
<li><a href="#orgb5dacc0">1.8. Template for has/read/write the numerical attribute</a></li>
<li><a href="#org0a63ace">1.9. Template for has/read/write the dataset of numerical data</a></li>
<li><a href="#org635f474">1.10. Template for has/read/write the dataset of strings</a></li>
<li><a href="#org3b0b722">1.11. Template for has/read/write the string attribute</a></li>
<li><a href="#org19ea838">1.12. RDM struct (hard-coded)</a>
<li><a href="#orgdccd6eb">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#org0a6a37c">1.2. Template for general structure in text back end</a></li>
<li><a href="#orgd8ccd61">1.3. Initialize function (constant part)</a></li>
<li><a href="#orgc5dc0f3">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#org3cf22af">1.5. Template for text read struct</a></li>
<li><a href="#org1d1e493">1.6. Template for text flush struct</a></li>
<li><a href="#org5b2a06a">1.7. Template for text free memory</a></li>
<li><a href="#orgff945a7">1.8. Template for has/read/write the numerical attribute</a></li>
<li><a href="#org8210d09">1.9. Template for has/read/write the dataset of numerical data</a></li>
<li><a href="#org0c8d455">1.10. Template for has/read/write the dataset of strings</a></li>
<li><a href="#org09713ab">1.11. Template for has/read/write the string attribute</a></li>
<li><a href="#org55c8dc8">1.12. RDM struct (hard-coded)</a>
<ul>
<li><a href="#org401fd65">1.12.1. Read the complete struct</a></li>
<li><a href="#org51dc782">1.12.2. Flush the complete struct</a></li>
<li><a href="#org36ab6bf">1.12.3. Free memory</a></li>
<li><a href="#orgfbfab87">1.12.4. Read/Write the one<sub>e</sub> attribute</a></li>
<li><a href="#org0cfe641">1.12.5. Read/Write the two<sub>e</sub> attribute</a></li>
<li><a href="#org16fa329">1.12.1. Read the complete struct</a></li>
<li><a href="#orgbe3a679">1.12.2. Flush the complete struct</a></li>
<li><a href="#org28391c1">1.12.3. Free memory</a></li>
<li><a href="#org67a9bea">1.12.4. Read/Write the one<sub>e</sub> attribute</a></li>
<li><a href="#org542629a">1.12.5. Read/Write the two<sub>e</sub> attribute</a></li>
</ul>
</li>
</ul>
@ -339,8 +339,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org648530d" class="outline-2">
<h2 id="org648530d"><span class="section-number-2">1</span> TEXT back end</h2>
<div id="outline-container-orgaa7d394" class="outline-2">
<h2 id="orgaa7d394"><span class="section-number-2">1</span> TEXT back end</h2>
<div class="outline-text-2" id="text-1">
<p>
The "file" produced by the text back end is a directory with one
@ -361,8 +361,8 @@ The file is written when closed, or when the flush function is called.
</p>
</div>
<div id="outline-container-org5e031d6" class="outline-3">
<h3 id="org5e031d6"><span class="section-number-3">1.1</span> Template for group-related structures in text back end</h3>
<div id="outline-container-orgdccd6eb" class="outline-3">
<h3 id="orgdccd6eb"><span class="section-number-3">1.1</span> Template for group-related structures in text back end</h3>
<div class="outline-text-3" id="text-1-1">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> $group$_s {
@ -381,8 +381,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-org7abf142" class="outline-3">
<h3 id="org7abf142"><span class="section-number-3">1.2</span> Template for general structure in text back end</h3>
<div id="outline-container-org0a6a37c" class="outline-3">
<h3 id="org0a6a37c"><span class="section-number-3">1.2</span> Template for general structure in text back end</h3>
<div class="outline-text-3" id="text-1-2">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> <span style="color: #228b22;">rdm_s</span> {
@ -408,8 +408,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-org4586757" class="outline-3">
<h3 id="org4586757"><span class="section-number-3">1.3</span> Initialize function (constant part)</h3>
<div id="outline-container-orgd8ccd61" class="outline-3">
<h3 id="orgd8ccd61"><span class="section-number-3">1.3</span> Initialize function (constant part)</h3>
<div class="outline-text-3" id="text-1-3">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -540,8 +540,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-orgec78b04" class="outline-3">
<h3 id="orgec78b04"><span class="section-number-3">1.4</span> Deinitialize function (templated part)</h3>
<div id="outline-container-orgc5dc0f3" class="outline-3">
<h3 id="orgc5dc0f3"><span class="section-number-3">1.4</span> Deinitialize function (templated part)</h3>
<div class="outline-text-3" id="text-1-4">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -566,8 +566,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-org240b0c4" class="outline-3">
<h3 id="org240b0c4"><span class="section-number-3">1.5</span> Template for text read struct</h3>
<div id="outline-container-org3cf22af" class="outline-3">
<h3 id="org3cf22af"><span class="section-number-3">1.5</span> Template for text read struct</h3>
<div class="outline-text-3" id="text-1-5">
<div class="org-src-container">
<pre class="src src-c">$group$_t*
@ -861,8 +861,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-orgabab9a1" class="outline-3">
<h3 id="orgabab9a1"><span class="section-number-3">1.6</span> Template for text flush struct</h3>
<div id="outline-container-org1d1e493" class="outline-3">
<h3 id="org1d1e493"><span class="section-number-3">1.6</span> Template for text flush struct</h3>
<div class="outline-text-3" id="text-1-6">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -927,8 +927,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org7e12d9b" class="outline-3">
<h3 id="org7e12d9b"><span class="section-number-3">1.7</span> Template for text free memory</h3>
<div id="outline-container-org5b2a06a" class="outline-3">
<h3 id="org5b2a06a"><span class="section-number-3">1.7</span> Template for text free memory</h3>
<div class="outline-text-3" id="text-1-7">
<p>
Memory is allocated when reading. The following function frees memory.
@ -973,8 +973,8 @@ Memory is allocated when reading. The following function frees memory.
</div>
</div>
<div id="outline-container-orgb5dacc0" class="outline-3">
<h3 id="orgb5dacc0"><span class="section-number-3">1.8</span> Template for has/read/write the numerical attribute</h3>
<div id="outline-container-orgff945a7" class="outline-3">
<h3 id="orgff945a7"><span class="section-number-3">1.8</span> Template for has/read/write the numerical attribute</h3>
<div class="outline-text-3" id="text-1-8">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1037,8 +1037,8 @@ Memory is allocated when reading. The following function frees memory.
</div>
</div>
<div id="outline-container-org0a63ace" class="outline-3">
<h3 id="org0a63ace"><span class="section-number-3">1.9</span> Template for has/read/write the dataset of numerical data</h3>
<div id="outline-container-org8210d09" class="outline-3">
<h3 id="org8210d09"><span class="section-number-3">1.9</span> Template for has/read/write the dataset of numerical data</h3>
<div class="outline-text-3" id="text-1-9">
<p>
The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1134,8 +1134,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org635f474" class="outline-3">
<h3 id="org635f474"><span class="section-number-3">1.10</span> Template for has/read/write the dataset of strings</h3>
<div id="outline-container-org0c8d455" class="outline-3">
<h3 id="org0c8d455"><span class="section-number-3">1.10</span> Template for has/read/write the dataset of strings</h3>
<div class="outline-text-3" id="text-1-10">
<p>
The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1236,8 +1236,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org3b0b722" class="outline-3">
<h3 id="org3b0b722"><span class="section-number-3">1.11</span> Template for has/read/write the string attribute</h3>
<div id="outline-container-org09713ab" class="outline-3">
<h3 id="org09713ab"><span class="section-number-3">1.11</span> Template for has/read/write the string attribute</h3>
<div class="outline-text-3" id="text-1-11">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1311,12 +1311,12 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org19ea838" class="outline-3">
<h3 id="org19ea838"><span class="section-number-3">1.12</span> RDM struct (hard-coded)</h3>
<div id="outline-container-org55c8dc8" class="outline-3">
<h3 id="org55c8dc8"><span class="section-number-3">1.12</span> RDM struct (hard-coded)</h3>
<div class="outline-text-3" id="text-1-12">
</div>
<div id="outline-container-org401fd65" class="outline-4">
<h4 id="org401fd65"><span class="section-number-4">1.12.1</span> Read the complete struct</h4>
<div id="outline-container-org16fa329" class="outline-4">
<h4 id="org16fa329"><span class="section-number-4">1.12.1</span> Read the complete struct</h4>
<div class="outline-text-4" id="text-1-12-1">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">rdm_t</span>* <span style="color: #0000ff;">trexio_text_read_rdm</span>(<span style="color: #228b22;">trexio_text_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>);
@ -1411,8 +1411,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
<div id="outline-container-org51dc782" class="outline-4">
<h4 id="org51dc782"><span class="section-number-4">1.12.2</span> Flush the complete struct</h4>
<div id="outline-container-orgbe3a679" class="outline-4">
<h4 id="orgbe3a679"><span class="section-number-4">1.12.2</span> Flush the complete struct</h4>
<div class="outline-text-4" id="text-1-12-2">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span> <span style="color: #0000ff;">trexio_text_flush_rdm</span>(<span style="color: #228b22;">trexio_text_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>);
@ -1454,8 +1454,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
<div id="outline-container-org36ab6bf" class="outline-4">
<h4 id="org36ab6bf"><span class="section-number-4">1.12.3</span> Free memory</h4>
<div id="outline-container-org28391c1" class="outline-4">
<h4 id="org28391c1"><span class="section-number-4">1.12.3</span> Free memory</h4>
<div class="outline-text-4" id="text-1-12-3">
<p>
Memory is allocated when reading. The followig function frees memory.
@ -1491,8 +1491,8 @@ Memory is allocated when reading. The followig function frees memory.
</div>
</div>
<div id="outline-container-orgfbfab87" class="outline-4">
<h4 id="orgfbfab87"><span class="section-number-4">1.12.4</span> Read/Write the one<sub>e</sub> attribute</h4>
<div id="outline-container-org67a9bea" class="outline-4">
<h4 id="org67a9bea"><span class="section-number-4">1.12.4</span> Read/Write the one<sub>e</sub> attribute</h4>
<div class="outline-text-4" id="text-1-12-4">
<p>
The <code>one_e</code> array is assumed allocated with the appropriate size.
@ -1558,8 +1558,8 @@ The <code>one_e</code> array is assumed allocated with the appropriate size.
</div>
</div>
<div id="outline-container-org0cfe641" class="outline-4">
<h4 id="org0cfe641"><span class="section-number-4">1.12.5</span> Read/Write the two<sub>e</sub> attribute</h4>
<div id="outline-container-org542629a" class="outline-4">
<h4 id="org542629a"><span class="section-number-4">1.12.5</span> Read/Write the two<sub>e</sub> attribute</h4>
<div class="outline-text-4" id="text-1-12-5">
<p>
<code>two_e</code> is a sparse data structure, which can be too large to fit
@ -1667,7 +1667,7 @@ file for each sparse float structure.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2021-10-25 Mon 11:40</p>
<p class="date">Created: 2021-10-25 Mon 15:00</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

120
trex.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>
<!-- 2021-10-25 Mon 11:40 -->
<!-- 2021-10-25 Mon 15:00 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREX Configuration file</title>
@ -333,33 +333,33 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgdbb693a">1. Metadata (metadata group)</a></li>
<li><a href="#orgaa3657f">2. Electron (electron group)</a></li>
<li><a href="#orgfb77207">3. Nucleus (nucleus group)</a></li>
<li><a href="#org296dd24">4. Effective core potentials (ecp group)</a>
<li><a href="#orga6493ca">1. Metadata (metadata group)</a></li>
<li><a href="#orge2ec59e">2. Electron (electron group)</a></li>
<li><a href="#org56dcc50">3. Nucleus (nucleus group)</a></li>
<li><a href="#org9eb1c49">4. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org0ef06fa">4.1. Example</a></li>
<li><a href="#orga4fab01">4.1. Example</a></li>
</ul>
</li>
<li><a href="#orgf927dde">5. Basis set (basis group)</a>
<li><a href="#org26f5cd8">5. Basis set (basis group)</a>
<ul>
<li><a href="#orge1d1b64">5.1. Example</a></li>
<li><a href="#org2248f8a">5.1. Example</a></li>
</ul>
</li>
<li><a href="#org6e26c51">6. Atomic orbitals (ao group)</a>
<li><a href="#orgbcdac54">6. Atomic orbitals (ao group)</a>
<ul>
<li><a href="#ao_one_e">6.1. One-electron integrals (<code>ao_1e_int</code> group)</a></li>
<li><a href="#ao_two_e">6.2. Two-electron integrals (<code>ao_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#org5e5bd84">7. Molecular orbitals (mo group)</a>
<li><a href="#orgbbdf51a">7. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#orga3fea09">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org69e9732">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org4be9962">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgdf049fa">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#org89e49af">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#orgf2ac79a">9. <span class="todo TODO">TODO</span> Reduced density matrices (rdm group)</a></li>
<li><a href="#orgc9f42fc">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#orge085214">9. <span class="todo TODO">TODO</span> Reduced density matrices (rdm group)</a></li>
</ul>
</div>
</div>
@ -399,8 +399,8 @@ arrays are 0-based. Hence, we introduce the <code>index</code> type which is an
1-based <code>int</code> in the Fortran interface and 0-based otherwise.
</p>
<div id="outline-container-orgdbb693a" class="outline-2">
<h2 id="orgdbb693a"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-orga6493ca" class="outline-2">
<h2 id="orga6493ca"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div class="outline-text-2" id="text-1">
<p>
As we expect our files to be archived in open-data repositories, we
@ -410,7 +410,7 @@ which have participated to the creation of the file, a list of
authors of the file, and a textual description.
</p>
<table id="org845cb4c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org954829c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -477,15 +477,15 @@ authors of the file, and a textual description.
</div>
</div>
<div id="outline-container-orgaa3657f" class="outline-2">
<h2 id="orgaa3657f"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div id="outline-container-orge2ec59e" class="outline-2">
<h2 id="orge2ec59e"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div class="outline-text-2" id="text-2">
<p>
We consider wave functions expressed in the spin-free formalism, where
the number of &uarr; and &darr; electrons is fixed.
</p>
<table id="org5e275fe" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org6d5bd9e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -524,15 +524,15 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-orgfb77207" class="outline-2">
<h2 id="orgfb77207"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div id="outline-container-org56dcc50" class="outline-2">
<h2 id="org56dcc50"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div class="outline-text-2" id="text-3">
<p>
The nuclei are considered as fixed point charges. Coordinates are
given in Cartesian \((x,y,z)\) format.
</p>
<table id="org88bb545" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5a5dcc6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -592,8 +592,8 @@ given in Cartesian \((x,y,z)\) format.
</div>
</div>
<div id="outline-container-org296dd24" class="outline-2">
<h2 id="org296dd24"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div id="outline-container-org9eb1c49" class="outline-2">
<h2 id="org9eb1c49"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div class="outline-text-2" id="text-4">
<p>
An effective core potential (ECP) \(V_A^{\text{ECP}}\) replacing the
@ -626,7 +626,7 @@ The functions \(V_{A\ell}\) are parameterized as:
See <a href="http://dx.doi.org/10.1063/1.4984046">http://dx.doi.org/10.1063/1.4984046</a> or <a href="https://doi.org/10.1063/1.5121006">https://doi.org/10.1063/1.5121006</a> for more info.
</p>
<table id="orgfd8a8b2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga649329" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -724,8 +724,8 @@ The latter causes issues when written before <code>ang_mom</code> in the TREXIO
</p>
</div>
<div id="outline-container-org0ef06fa" class="outline-3">
<h3 id="org0ef06fa"><span class="section-number-3">4.1</span> Example</h3>
<div id="outline-container-orga4fab01" class="outline-3">
<h3 id="orga4fab01"><span class="section-number-3">4.1</span> Example</h3>
<div class="outline-text-3" id="text-4-1">
<p>
For example, consider H<sub>2</sub> molecule with the following
@ -750,8 +750,8 @@ In TREXIO representation this would be:
<pre class="example">
num = 8
# lmax+1 per atom
max_ang_mom_plus_1 = [ 1, 1 ]
# lmax+1 per atom: 0 here because no core electrons to be removed
max_ang_mom_plus_1 = [ 0, 0 ]
# number of core electrons to remove per atom
zcore = [ 0, 0 ]
@ -788,8 +788,8 @@ power = [
</div>
</div>
<div id="outline-container-orgf927dde" class="outline-2">
<h2 id="orgf927dde"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div id="outline-container-org26f5cd8" class="outline-2">
<h2 id="org26f5cd8"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div class="outline-text-2" id="text-5">
<p>
We consider here basis functions centered on nuclei. Hence, we enable
@ -842,7 +842,7 @@ If the the basis function is not considered normalized, \(\mathcal{N}_s=1\).
All the basis set parameters are stored in one-dimensional arrays:
</p>
<table id="org117b345" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgcbe6c25" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -936,8 +936,8 @@ All the basis set parameters are stored in one-dimensional arrays:
</table>
</div>
<div id="outline-container-orge1d1b64" class="outline-3">
<h3 id="orge1d1b64"><span class="section-number-3">5.1</span> Example</h3>
<div id="outline-container-org2248f8a" class="outline-3">
<h3 id="org2248f8a"><span class="section-number-3">5.1</span> Example</h3>
<div class="outline-text-3" id="text-5-1">
<p>
For example, consider H<sub>2</sub> with the following basis set (in GAMESS
@ -1015,8 +1015,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-org6e26c51" class="outline-2">
<h2 id="org6e26c51"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div id="outline-container-orgbcdac54" class="outline-2">
<h2 id="orgbcdac54"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div class="outline-text-2" id="text-6">
<p>
Going from the atomic basis set to AOs implies a systematic
@ -1064,13 +1064,13 @@ shell, as in the GAMESS convention where
<p>
In such a case, one should set the normalization of the shell (in
the <a href="#orgf927dde">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#org26f5cd8">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
normalization factor of the atomic orbitals in spherical coordinates.
The normalization factor of the \(xy\) function which should be
introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
</p>
<table id="org34d89b7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc58a3e5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1122,8 +1122,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
</table>
</div>
<div id="outline-container-org85101eb" class="outline-3">
<h3 id="ao_one_e"><a id="org85101eb"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div id="outline-container-org7d5fb99" class="outline-3">
<h3 id="ao_one_e"><a id="org7d5fb99"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div class="outline-text-3" id="text-ao_one_e">
<ul class="org-ul">
<li>\[ \hat{V}_{\text{ne}} = \sum_{A=1}^{N_\text{nucl}}
@ -1141,7 +1141,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="orgd651eec" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org91ae93c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1208,8 +1208,8 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-orgbaa5f5c" class="outline-3">
<h3 id="ao_two_e"><a id="orgbaa5f5c"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div id="outline-container-org1d2373e" class="outline-3">
<h3 id="ao_two_e"><a id="org1d2373e"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div class="outline-text-3" id="text-ao_two_e">
<p>
The two-electron integrals for a two-electron operator \(\hat{O}\) are
@ -1230,7 +1230,7 @@ notation.
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
</ul>
<table id="org7df47e3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgbc3d359" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1270,10 +1270,10 @@ notation.
</div>
</div>
<div id="outline-container-org5e5bd84" class="outline-2">
<h2 id="org5e5bd84"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div id="outline-container-orgbbdf51a" class="outline-2">
<h2 id="orgbbdf51a"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div class="outline-text-2" id="text-7">
<table id="orgcda49fb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgdc6666c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1339,8 +1339,8 @@ notation.
</table>
</div>
<div id="outline-container-orga3fea09" class="outline-3">
<h3 id="orga3fea09"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div id="outline-container-org4be9962" class="outline-3">
<h3 id="org4be9962"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div class="outline-text-3" id="text-7-1">
<p>
The operators as the same as those defined in the
@ -1348,7 +1348,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org93a0d8b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org02a49a0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1415,8 +1415,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org69e9732" class="outline-3">
<h3 id="org69e9732"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div id="outline-container-orgdf049fa" class="outline-3">
<h3 id="orgdf049fa"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div class="outline-text-3" id="text-7-2">
<p>
The operators as the same as those defined in the
@ -1424,7 +1424,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org6b8c051" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org86aba12" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1464,13 +1464,13 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org89e49af" class="outline-2">
<h2 id="org89e49af"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
<div id="outline-container-orgc9f42fc" class="outline-2">
<h2 id="orgc9f42fc"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
</div>
<div id="outline-container-orgf2ac79a" class="outline-2">
<h2 id="orgf2ac79a"><span class="section-number-2">9</span> <span class="todo TODO">TODO</span> Reduced density matrices (rdm group)</h2>
<div id="outline-container-orge085214" class="outline-2">
<h2 id="orge085214"><span class="section-number-2">9</span> <span class="todo TODO">TODO</span> Reduced density matrices (rdm group)</h2>
<div class="outline-text-2" id="text-9">
<table id="orgaeb15bf" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org6503f17" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1525,7 +1525,7 @@ the basis of molecular orbitals.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2021-10-25 Mon 11:40</p>
<p class="date">Created: 2021-10-25 Mon 15:00</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>