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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>
<!-- 2021-11-18 Thu 13:35 -->
<!-- 2021-11-18 Thu 15:47 -->
<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: 2021-11-18 Thu 13:35</p>
<p class="date">Created: 2021-11-18 Thu 15:47</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>
<!-- 2021-11-18 Thu 13:35 -->
<!-- 2021-11-18 Thu 15:47 -->
<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="#org7485b1c">1. Text back end</a></li>
<li><a href="#org6deefd8">2. HDF5 Back end</a></li>
<li><a href="#orge046e0d">1. Text back end</a></li>
<li><a href="#orgf61d83e">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-org7485b1c" class="outline-2">
<h2 id="org7485b1c"><span class="section-number-2">1</span> Text back end</h2>
<div id="outline-container-orge046e0d" class="outline-2">
<h2 id="orge046e0d"><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-org6deefd8" class="outline-2">
<h2 id="org6deefd8"><span class="section-number-2">2</span> HDF5 Back end</h2>
<div id="outline-container-orgf61d83e" class="outline-2">
<h2 id="orgf61d83e"><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: 2021-11-18 Thu 13:35</p>
<p class="date">Created: 2021-11-18 Thu 15:47</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>
<!-- 2021-11-18 Thu 13:35 -->
<!-- 2021-11-18 Thu 15:47 -->
<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: 2021-11-18 Thu 13:35</p>
<p class="date">Created: 2021-11-18 Thu 15:47</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>
<!-- 2021-11-18 Thu 13:35 -->
<!-- 2021-11-18 Thu 15:47 -->
<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="#org95ef7e4">1. Coding conventions</a>
<li><a href="#org990cbc3">1. Coding conventions</a>
<ul>
<li><a href="#org0f7366f">1.1. Memory allocation</a></li>
<li><a href="#org85dcc30">1.1. Memory allocation</a></li>
</ul>
</li>
<li><a href="#org3a8ff76">2. Front end</a>
<li><a href="#org89eef92">2. Front end</a>
<ul>
<li><a href="#org1c5d76f">2.1. Error handling</a>
<li><a href="#org4235dfe">2.1. Error handling</a>
<ul>
<li><a href="#org17b757c">2.1.1. Decoding errors</a>
<li><a href="#org536377a">2.1.1. Decoding errors</a>
<ul>
<li><a href="#org6edcfb5">2.1.1.1. C source code</a></li>
<li><a href="#orgfff80d8">2.1.1.2. Fortran interface</a></li>
<li><a href="#orgcf64689">2.1.1.3. Python interface</a></li>
<li><a href="#orgc1dc5e3">2.1.1.1. C source code</a></li>
<li><a href="#orgb4878e0">2.1.1.2. Fortran interface</a></li>
<li><a href="#org33f1372">2.1.1.3. Python interface</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org8496948">2.2. Back ends</a>
<li><a href="#org504e92f">2.2. Back ends</a>
<ul>
<li><a href="#org9dd90fb">2.2.1. C</a></li>
<li><a href="#org850cbaf">2.2.2. Fortran</a></li>
<li><a href="#orgc3efc40">2.2.3. Python</a></li>
<li><a href="#org1eee5ce">2.2.1. C</a></li>
<li><a href="#org5972f6f">2.2.2. Fortran</a></li>
<li><a href="#orge924331">2.2.3. Python</a></li>
</ul>
</li>
<li><a href="#org38e2030">2.3. Read/write behavior</a></li>
<li><a href="#orgc0c152d">2.4. TREXIO file type</a>
<li><a href="#org4e02973">2.3. Read/write behavior</a></li>
<li><a href="#orgcb017f2">2.4. TREXIO file type</a>
<ul>
<li><a href="#orge61ef47">2.4.1. TREXIO<sub>File</sub> Python class</a></li>
<li><a href="#org6363daf">2.4.1. TREXIO<sub>File</sub> Python class</a></li>
</ul>
</li>
<li><a href="#orgc1ed07b">2.5. Polymorphism of the file handle</a></li>
<li><a href="#orgd948212">2.6. File opening</a>
<li><a href="#org90972ec">2.5. Polymorphism of the file handle</a></li>
<li><a href="#orgfd4a623">2.6. File opening</a>
<ul>
<li><a href="#org3f7d397">2.6.1. C</a></li>
<li><a href="#org09252d5">2.6.2. Fortran</a></li>
<li><a href="#org31dd44d">2.6.3. Python</a></li>
<li><a href="#org59be5ec">2.6.4. Zero-based versus one-based arrays of indices</a></li>
<li><a href="#orgc41f30d">2.6.1. C</a></li>
<li><a href="#orgcd60558">2.6.2. Fortran</a></li>
<li><a href="#orgd6e65c2">2.6.3. Python</a></li>
<li><a href="#orga1fa7f2">2.6.4. Zero-based versus one-based arrays of indices</a></li>
</ul>
</li>
<li><a href="#org91bf330">2.7. File closing</a>
<li><a href="#org85cbbca">2.7. File closing</a>
<ul>
<li><a href="#orgc92dfd1">2.7.1. C</a></li>
<li><a href="#orgdfd57c6">2.7.2. Fortran</a></li>
<li><a href="#orge5adb60">2.7.3. Python</a></li>
<li><a href="#org0517d5e">2.7.1. C</a></li>
<li><a href="#org0d1a2d1">2.7.2. Fortran</a></li>
<li><a href="#org445b1bd">2.7.3. Python</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org6984aec">3. Templates for front end</a>
<li><a href="#org1e9cbbd">3. Templates for front end</a>
<ul>
<li><a href="#orge8075eb">3.1. Description</a></li>
<li><a href="#org59399a5">3.2. Templates for front end has/read/write a single numerical attribute</a>
<li><a href="#org57ea452">3.1. Description</a></li>
<li><a href="#org93d2b25">3.2. Templates for front end has/read/write a single numerical attribute</a>
<ul>
<li><a href="#org5cac91b">3.2.1. Introduction</a></li>
<li><a href="#orgb8ee39d">3.2.2. C templates for front end</a>
<li><a href="#orga1985ff">3.2.1. Introduction</a></li>
<li><a href="#org89aa403">3.2.2. C templates for front end</a>
<ul>
<li><a href="#org26bc1a3">3.2.2.1. Function declarations</a></li>
<li><a href="#orga4db47e">3.2.2.2. Source code for double precision functions</a></li>
<li><a href="#orgbd23d89">3.2.2.3. Source code for single precision functions</a></li>
<li><a href="#orgafe0585">3.2.2.4. Source code for default functions</a></li>
<li><a href="#orgb040818">3.2.2.1. Function declarations</a></li>
<li><a href="#org5188898">3.2.2.2. Source code for double precision functions</a></li>
<li><a href="#orgbca48e3">3.2.2.3. Source code for single precision functions</a></li>
<li><a href="#orgdb0a3cf">3.2.2.4. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#orgc9f9e14">3.2.3. Fortran templates for front end</a></li>
<li><a href="#orgb927b84">3.2.4. Python templates for front end</a></li>
<li><a href="#org92dcf51">3.2.3. Fortran templates for front end</a></li>
<li><a href="#orga37da32">3.2.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#orga16049e">3.3. Templates for front end has/read/write a dataset of numerical data</a>
<li><a href="#org53f898f">3.3. Templates for front end has/read/write a dataset of numerical data</a>
<ul>
<li><a href="#orge8f8a31">3.3.1. Introduction</a></li>
<li><a href="#orgb83ec54">3.3.2. C templates for front end</a>
<li><a href="#org04892f9">3.3.1. Introduction</a></li>
<li><a href="#org050a68a">3.3.2. C templates for front end</a>
<ul>
<li><a href="#org0bc6934">3.3.2.1. Function declarations</a></li>
<li><a href="#org57246e8">3.3.2.2. Source code for double precision functions</a></li>
<li><a href="#org308bfb1">3.3.2.3. Source code for single precision functions</a></li>
<li><a href="#org16b314b">3.3.2.4. Source code for memory-safe functions</a></li>
<li><a href="#orga33275e">3.3.2.5. Source code for default functions</a></li>
<li><a href="#orgadd038e">3.3.2.1. Function declarations</a></li>
<li><a href="#org4fa68dc">3.3.2.2. Source code for double precision functions</a></li>
<li><a href="#org1f08881">3.3.2.3. Source code for single precision functions</a></li>
<li><a href="#org89c76c1">3.3.2.4. Source code for memory-safe functions</a></li>
<li><a href="#orgdd7fa8b">3.3.2.5. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#org49f2b89">3.3.3. Fortran templates for front end</a></li>
<li><a href="#org75cea83">3.3.4. Python templates for front end</a></li>
<li><a href="#org6877c97">3.3.3. Fortran templates for front end</a></li>
<li><a href="#orgafaa86e">3.3.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#org43d6c25">3.4. Sparse data structures</a></li>
<li><a href="#org366960b">3.5. Templates for front end has/read/write a dataset of strings</a>
<li><a href="#orgefc94c8">3.4. Sparse data structures</a></li>
<li><a href="#org39ff1e7">3.5. Templates for front end has/read/write a dataset of strings</a>
<ul>
<li><a href="#orgdab245a">3.5.1. Introduction</a></li>
<li><a href="#orga148f43">3.5.2. C templates for front end</a>
<li><a href="#org9475ff1">3.5.1. Introduction</a></li>
<li><a href="#org8fc6f53">3.5.2. C templates for front end</a>
<ul>
<li><a href="#org22317ad">3.5.2.1. Function declarations</a></li>
<li><a href="#org8994510">3.5.2.2. Source code for default functions</a></li>
<li><a href="#orgefaf4f8">3.5.2.1. Function declarations</a></li>
<li><a href="#orga7b6974">3.5.2.2. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#org395ca87">3.5.3. Fortran templates for front end</a></li>
<li><a href="#org90301e9">3.5.4. Python templates for front end</a></li>
<li><a href="#org137db32">3.5.3. Fortran templates for front end</a></li>
<li><a href="#orgdef3333">3.5.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#orgaa970de">3.6. Templates for front end has/read/write a single string attribute</a>
<li><a href="#orgd8e293b">3.6. Templates for front end has/read/write a single string attribute</a>
<ul>
<li><a href="#org291604e">3.6.1. Introduction</a></li>
<li><a href="#orge17cbc3">3.6.2. C templates for front end</a>
<li><a href="#org06fb00c">3.6.1. Introduction</a></li>
<li><a href="#orgb4a98df">3.6.2. C templates for front end</a>
<ul>
<li><a href="#org46e8123">3.6.2.1. Function declarations</a></li>
<li><a href="#org6bc70d5">3.6.2.2. Source code for default functions</a></li>
<li><a href="#orgc6fc2a3">3.6.2.1. Function declarations</a></li>
<li><a href="#org23d194f">3.6.2.2. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#orgf559a3e">3.6.3. Fortran templates for front end</a></li>
<li><a href="#org4db1c04">3.6.4. Python templates for front end</a></li>
<li><a href="#org9c41a8c">3.6.3. Fortran templates for front end</a></li>
<li><a href="#org7837d60">3.6.4. Python templates for front end</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orged0ae67">4. Fortran helper/wrapper functions</a></li>
<li><a href="#org9c14c96">4. Fortran helper/wrapper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-org95ef7e4" class="outline-2">
<h2 id="org95ef7e4"><span class="section-number-2">1</span> Coding conventions</h2>
<div id="outline-container-org990cbc3" class="outline-2">
<h2 id="org990cbc3"><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-org0f7366f" class="outline-3">
<h3 id="org0f7366f"><span class="section-number-3">1.1</span> Memory allocation</h3>
<div id="outline-container-org85dcc30" class="outline-3">
<h3 id="org85dcc30"><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-org3a8ff76" class="outline-2">
<h2 id="org3a8ff76"><span class="section-number-2">2</span> Front end</h2>
<div id="outline-container-org89eef92" class="outline-2">
<h2 id="org89eef92"><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-org1c5d76f" class="outline-3">
<h3 id="org1c5d76f"><span class="section-number-3">2.1</span> Error handling</h3>
<div id="outline-container-org4235dfe" class="outline-3">
<h3 id="org4235dfe"><span class="section-number-3">2.1</span> Error handling</h3>
<div class="outline-text-3" id="text-2-1">
<table id="org49b11f8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgde27f8a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -742,8 +742,8 @@ TREXIO front end is modular, which simplifies implementation of new back ends.
</div>
</div>
<div id="outline-container-org17b757c" class="outline-4">
<h4 id="org17b757c"><span class="section-number-4">2.1.1</span> Decoding errors</h4>
<div id="outline-container-org536377a" class="outline-4">
<h4 id="org536377a"><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
@ -766,8 +766,8 @@ The text strings are extracted from the previous table.
</p>
</div>
<div id="outline-container-org6edcfb5" class="outline-5">
<h5 id="org6edcfb5"><span class="section-number-5">2.1.1.1</span> C source code</h5>
<div id="outline-container-orgc1dc5e3" class="outline-5">
<h5 id="orgc1dc5e3"><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>*
@ -875,8 +875,8 @@ The text strings are extracted from the previous table.
</div>
</div>
<div id="outline-container-orgfff80d8" class="outline-5">
<h5 id="orgfff80d8"><span class="section-number-5">2.1.1.2</span> Fortran interface</h5>
<div id="outline-container-orgb4878e0" class="outline-5">
<h5 id="orgb4878e0"><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>
@ -892,8 +892,8 @@ The text strings are extracted from the previous table.
</div>
</div>
<div id="outline-container-orgcf64689" class="outline-5">
<h5 id="orgcf64689"><span class="section-number-5">2.1.1.3</span> Python interface</h5>
<div id="outline-container-org33f1372" class="outline-5">
<h5 id="org33f1372"><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>):
@ -932,8 +932,8 @@ The text strings are extracted from the previous table.
</div>
</div>
<div id="outline-container-org8496948" class="outline-3">
<h3 id="org8496948"><span class="section-number-3">2.2</span> Back ends</h3>
<div id="outline-container-org504e92f" class="outline-3">
<h3 id="org504e92f"><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:
@ -957,8 +957,8 @@ lines that correspond to the <code>TREXIO_JSON</code> back end (not implemented
</p>
</div>
<div id="outline-container-org9dd90fb" class="outline-4">
<h4 id="org9dd90fb"><span class="section-number-4">2.2.1</span> C</h4>
<div id="outline-container-org1eee5ce" class="outline-4">
<h4 id="org1eee5ce"><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>;
@ -1001,8 +1001,8 @@ This is useful due to the fact that HDF5 back end can be disabled at configure s
</div>
</div>
<div id="outline-container-org850cbaf" class="outline-4">
<h4 id="org850cbaf"><span class="section-number-4">2.2.2</span> Fortran</h4>
<div id="outline-container-org5972f6f" class="outline-4">
<h4 id="org5972f6f"><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>
@ -1028,8 +1028,8 @@ The function below is a Fortran interface for the aforementioned C-compatible <c
</div>
</div>
<div id="outline-container-orgc3efc40" class="outline-4">
<h4 id="orgc3efc40"><span class="section-number-4">2.2.3</span> Python</h4>
<div id="outline-container-orge924331" class="outline-4">
<h4 id="orge924331"><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>
@ -1043,8 +1043,8 @@ The function below is a Fortran interface for the aforementioned C-compatible <c
</div>
</div>
<div id="outline-container-org38e2030" class="outline-3">
<h3 id="org38e2030"><span class="section-number-3">2.3</span> Read/write behavior</h3>
<div id="outline-container-org4e02973" class="outline-3">
<h3 id="org4e02973"><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
@ -1072,8 +1072,8 @@ concurrent programs, the behavior is not specified.
</p>
</div>
</div>
<div id="outline-container-orgc0c152d" class="outline-3">
<h3 id="orgc0c152d"><span class="section-number-3">2.4</span> TREXIO file type</h3>
<div id="outline-container-orgcb017f2" class="outline-3">
<h3 id="orgcb017f2"><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
@ -1107,8 +1107,8 @@ TREXIO files will have as a first argument the TREXIO file handle.
</div>
</div>
<div id="outline-container-orge61ef47" class="outline-4">
<h4 id="orge61ef47"><span class="section-number-4">2.4.1</span> TREXIO<sub>File</sub> Python class</h4>
<div id="outline-container-org6363daf" class="outline-4">
<h4 id="org6363daf"><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>:
@ -1181,8 +1181,8 @@ TREXIO files will have as a first argument the TREXIO file handle.
</div>
</div>
<div id="outline-container-orgc1ed07b" class="outline-3">
<h3 id="orgc1ed07b"><span class="section-number-3">2.5</span> Polymorphism of the file handle</h3>
<div id="outline-container-org90972ec" class="outline-3">
<h3 id="org90972ec"><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
@ -1201,8 +1201,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-orgd948212" class="outline-3">
<h3 id="orgd948212"><span class="section-number-3">2.6</span> File opening</h3>
<div id="outline-container-orgfd4a623" class="outline-3">
<h3 id="orgfd4a623"><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.
@ -1241,8 +1241,8 @@ renaming the <code>.txt</code> data files.
</p>
</div>
<div id="outline-container-org3f7d397" class="outline-4">
<h4 id="org3f7d397"><span class="section-number-4">2.6.1</span> C</h4>
<div id="outline-container-orgc41f30d" class="outline-4">
<h4 id="orgc41f30d"><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>*
@ -1429,8 +1429,8 @@ renaming the <code>.txt</code> data files.
</div>
</div>
<div id="outline-container-org09252d5" class="outline-4">
<h4 id="org09252d5"><span class="section-number-4">2.6.2</span> Fortran</h4>
<div id="outline-container-orgcd60558" class="outline-4">
<h4 id="orgcd60558"><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>
@ -1448,8 +1448,8 @@ renaming the <code>.txt</code> data files.
</div>
</div>
<div id="outline-container-org31dd44d" class="outline-4">
<h4 id="org31dd44d"><span class="section-number-4">2.6.3</span> Python</h4>
<div id="outline-container-orgd6e65c2" class="outline-4">
<h4 id="orgd6e65c2"><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>):
@ -1497,8 +1497,8 @@ renaming the <code>.txt</code> data files.
</div>
</div>
<div id="outline-container-org59be5ec" class="outline-4">
<h4 id="org59be5ec"><span class="section-number-4">2.6.4</span> Zero-based versus one-based arrays of indices</h4>
<div id="outline-container-orga1fa7f2" class="outline-4">
<h4 id="orga1fa7f2"><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
@ -1531,8 +1531,8 @@ know if we need to shift by 1 arrays of indices.
</div>
</div>
<div id="outline-container-org91bf330" class="outline-3">
<h3 id="org91bf330"><span class="section-number-3">2.7</span> File closing</h3>
<div id="outline-container-org85cbbca" class="outline-3">
<h3 id="org85cbbca"><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.
@ -1549,8 +1549,8 @@ output:
</p>
</div>
<div id="outline-container-orgc92dfd1" class="outline-4">
<h4 id="orgc92dfd1"><span class="section-number-4">2.7.1</span> C</h4>
<div id="outline-container-org0517d5e" class="outline-4">
<h4 id="org0517d5e"><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>
@ -1629,8 +1629,8 @@ output:
</div>
</div>
<div id="outline-container-orgdfd57c6" class="outline-4">
<h4 id="orgdfd57c6"><span class="section-number-4">2.7.2</span> Fortran</h4>
<div id="outline-container-org0d1a2d1" class="outline-4">
<h4 id="org0d1a2d1"><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>
@ -1644,8 +1644,8 @@ output:
</div>
</div>
<div id="outline-container-orge5adb60" class="outline-4">
<h4 id="orge5adb60"><span class="section-number-4">2.7.3</span> Python</h4>
<div id="outline-container-org445b1bd" class="outline-4">
<h4 id="org445b1bd"><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):
@ -1667,12 +1667,12 @@ output:
</div>
</div>
<div id="outline-container-org6984aec" class="outline-2">
<h2 id="org6984aec"><span class="section-number-2">3</span> Templates for front end</h2>
<div id="outline-container-org1e9cbbd" class="outline-2">
<h2 id="org1e9cbbd"><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-orge8075eb" class="outline-3">
<h3 id="orge8075eb"><span class="section-number-3">3.1</span> Description</h3>
<div id="outline-container-org57ea452" class="outline-3">
<h3 id="org57ea452"><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>:
@ -1893,12 +1893,12 @@ value will result in <code>TREXIO_INVALID_ARG_2</code> exit code.
</div>
</div>
<div id="outline-container-org59399a5" class="outline-3">
<h3 id="org59399a5"><span class="section-number-3">3.2</span> Templates for front end has/read/write a single numerical attribute</h3>
<div id="outline-container-org93d2b25" class="outline-3">
<h3 id="org93d2b25"><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-org5cac91b" class="outline-4">
<h4 id="org5cac91b"><span class="section-number-4">3.2.1</span> Introduction</h4>
<div id="outline-container-orga1985ff" class="outline-4">
<h4 id="orga1985ff"><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,
@ -1969,8 +1969,8 @@ namely single value of int/float types.
</div>
</div>
<div id="outline-container-orgb8ee39d" class="outline-4">
<h4 id="orgb8ee39d"><span class="section-number-4">3.2.2</span> C templates for front end</h4>
<div id="outline-container-org89aa403" class="outline-4">
<h4 id="org89aa403"><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
@ -1984,12 +1984,12 @@ precision (see Table above).
</p>
</div>
<div id="outline-container-org26bc1a3" class="outline-5">
<h5 id="org26bc1a3"><span class="section-number-5">3.2.2.1</span> Function declarations</h5>
<div id="outline-container-orgb040818" class="outline-5">
<h5 id="orgb040818"><span class="section-number-5">3.2.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-orga4db47e" class="outline-5">
<h5 id="orga4db47e"><span class="section-number-5">3.2.2.2</span> Source code for double precision functions</h5>
<div id="outline-container-org5188898" class="outline-5">
<h5 id="org5188898"><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>
@ -2058,8 +2058,8 @@ precision (see Table above).
</div>
</div>
<div id="outline-container-orgbd23d89" class="outline-5">
<h5 id="orgbd23d89"><span class="section-number-5">3.2.2.3</span> Source code for single precision functions</h5>
<div id="outline-container-orgbca48e3" class="outline-5">
<h5 id="orgbca48e3"><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>
@ -2135,8 +2135,8 @@ precision (see Table above).
</div>
</div>
<div id="outline-container-orgafe0585" class="outline-5">
<h5 id="orgafe0585"><span class="section-number-5">3.2.2.4</span> Source code for default functions</h5>
<div id="outline-container-orgdb0a3cf" class="outline-5">
<h5 id="orgdb0a3cf"><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>
@ -2193,8 +2193,8 @@ precision (see Table above).
</div>
</div>
<div id="outline-container-orgc9f9e14" class="outline-4">
<h4 id="orgc9f9e14"><span class="section-number-4">3.2.3</span> Fortran templates for front end</h4>
<div id="outline-container-org92dcf51" class="outline-4">
<h4 id="org92dcf51"><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.
@ -2279,8 +2279,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-orgb927b84" class="outline-4">
<h4 id="orgb927b84"><span class="section-number-4">3.2.4</span> Python templates for front end</h4>
<div id="outline-container-orga37da32" class="outline-4">
<h4 id="orga37da32"><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>:
@ -2365,12 +2365,12 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-orga16049e" class="outline-3">
<h3 id="orga16049e"><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-org53f898f" class="outline-3">
<h3 id="org53f898f"><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-orge8f8a31" class="outline-4">
<h4 id="orge8f8a31"><span class="section-number-4">3.3.1</span> Introduction</h4>
<div id="outline-container-org04892f9" class="outline-4">
<h4 id="org04892f9"><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.
@ -2452,8 +2452,8 @@ This section concerns API calls related to datasets.
</div>
</div>
<div id="outline-container-orgb83ec54" class="outline-4">
<h4 id="orgb83ec54"><span class="section-number-4">3.3.2</span> C templates for front end</h4>
<div id="outline-container-org050a68a" class="outline-4">
<h4 id="org050a68a"><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.
@ -2464,13 +2464,13 @@ The basic (non-suffixed) API call on datasets deals with double precision (see T
</p>
</div>
<div id="outline-container-org0bc6934" class="outline-5">
<h5 id="org0bc6934"><span class="section-number-5">3.3.2.1</span> Function declarations</h5>
<div id="outline-container-orgadd038e" class="outline-5">
<h5 id="orgadd038e"><span class="section-number-5">3.3.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-org57246e8" class="outline-5">
<h5 id="org57246e8"><span class="section-number-5">3.3.2.2</span> Source code for double precision functions</h5>
<div id="outline-container-org4fa68dc" class="outline-5">
<h5 id="org4fa68dc"><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>
@ -2606,8 +2606,8 @@ The basic (non-suffixed) API call on datasets deals with double precision (see T
</div>
</div>
<div id="outline-container-org308bfb1" class="outline-5">
<h5 id="org308bfb1"><span class="section-number-5">3.3.2.3</span> Source code for single precision functions</h5>
<div id="outline-container-org1f08881" class="outline-5">
<h5 id="org1f08881"><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>
@ -2756,11 +2756,11 @@ The basic (non-suffixed) API call on datasets deals with double precision (see T
</div>
</div>
<div id="outline-container-org16b314b" class="outline-5">
<h5 id="org16b314b"><span class="section-number-5">3.3.2.4</span> Source code for memory-safe functions</h5>
<div id="outline-container-org89c76c1" class="outline-5">
<h5 id="org89c76c1"><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="orgd1bbe2e"><span style="color: #228b22;">trexio_exit_code</span> <span style="color: #a0522d;">rc</span>;
<pre class="src src-c" id="org3cdde7a"><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>*/
@ -2916,8 +2916,8 @@ rc = trexio_read_$group_dset_dim$_64(file, &amp;($group_dset_dim$));
</div>
</div>
<div id="outline-container-orga33275e" class="outline-5">
<h5 id="orga33275e"><span class="section-number-5">3.3.2.5</span> Source code for default functions</h5>
<div id="outline-container-orgdd7fa8b" class="outline-5">
<h5 id="orgdd7fa8b"><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>
@ -2995,8 +2995,8 @@ rc = trexio_read_$group_dset_dim$_64(file, &amp;($group_dset_dim$));
</div>
</div>
<div id="outline-container-org49f2b89" class="outline-4">
<h4 id="org49f2b89"><span class="section-number-4">3.3.3</span> Fortran templates for front end</h4>
<div id="outline-container-org6877c97" class="outline-4">
<h4 id="org6877c97"><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>.
@ -3081,8 +3081,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-org75cea83" class="outline-4">
<h4 id="org75cea83"><span class="section-number-4">3.3.4</span> Python templates for front end</h4>
<div id="outline-container-orgafaa86e" class="outline-4">
<h4 id="orgafaa86e"><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>:
@ -3277,8 +3277,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-org43d6c25" class="outline-3">
<h3 id="org43d6c25"><span class="section-number-3">3.4</span> Sparse data structures</h3>
<div id="outline-container-orgefc94c8" class="outline-3">
<h3 id="orgefc94c8"><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
@ -3419,12 +3419,12 @@ For the values,
</div>
</div>
<div id="outline-container-org366960b" class="outline-3">
<h3 id="org366960b"><span class="section-number-3">3.5</span> Templates for front end has/read/write a dataset of strings</h3>
<div id="outline-container-org39ff1e7" class="outline-3">
<h3 id="org39ff1e7"><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-orgdab245a" class="outline-4">
<h4 id="orgdab245a"><span class="section-number-4">3.5.1</span> Introduction</h4>
<div id="outline-container-org9475ff1" class="outline-4">
<h4 id="org9475ff1"><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.
@ -3464,8 +3464,8 @@ This section concerns API calls related to datasets of strings.
</div>
</div>
<div id="outline-container-orga148f43" class="outline-4">
<h4 id="orga148f43"><span class="section-number-4">3.5.2</span> C templates for front end</h4>
<div id="outline-container-org8fc6f53" class="outline-4">
<h4 id="org8fc6f53"><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
@ -3473,12 +3473,12 @@ to/from the <code>TREXIO</code> file (except for <code>trexio_has_</code> functi
</p>
</div>
<div id="outline-container-org22317ad" class="outline-5">
<h5 id="org22317ad"><span class="section-number-5">3.5.2.1</span> Function declarations</h5>
<div id="outline-container-orgefaf4f8" class="outline-5">
<h5 id="orgefaf4f8"><span class="section-number-5">3.5.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-org8994510" class="outline-5">
<h5 id="org8994510"><span class="section-number-5">3.5.2.2</span> Source code for default functions</h5>
<div id="outline-container-orga7b6974" class="outline-5">
<h5 id="orga7b6974"><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>
@ -3732,8 +3732,8 @@ to/from the <code>TREXIO</code> file (except for <code>trexio_has_</code> functi
</div>
</div>
<div id="outline-container-org395ca87" class="outline-4">
<h4 id="org395ca87"><span class="section-number-4">3.5.3</span> Fortran templates for front end</h4>
<div id="outline-container-org137db32" class="outline-4">
<h4 id="org137db32"><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>.
@ -3829,8 +3829,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-org90301e9" class="outline-4">
<h4 id="org90301e9"><span class="section-number-4">3.5.4</span> Python templates for front end</h4>
<div id="outline-container-orgdef3333" class="outline-4">
<h4 id="orgdef3333"><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>:
@ -3946,12 +3946,12 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-orgaa970de" class="outline-3">
<h3 id="orgaa970de"><span class="section-number-3">3.6</span> Templates for front end has/read/write a single string attribute</h3>
<div id="outline-container-orgd8e293b" class="outline-3">
<h3 id="orgd8e293b"><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-org291604e" class="outline-4">
<h4 id="org291604e"><span class="section-number-4">3.6.1</span> Introduction</h4>
<div id="outline-container-org06fb00c" class="outline-4">
<h4 id="org06fb00c"><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.
@ -3991,16 +3991,16 @@ This section concerns API calls related to string attributes.
</div>
</div>
<div id="outline-container-orge17cbc3" class="outline-4">
<h4 id="orge17cbc3"><span class="section-number-4">3.6.2</span> C templates for front end</h4>
<div id="outline-container-orgb4a98df" class="outline-4">
<h4 id="orgb4a98df"><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-org46e8123" class="outline-5">
<h5 id="org46e8123"><span class="section-number-5">3.6.2.1</span> Function declarations</h5>
<div id="outline-container-orgc6fc2a3" class="outline-5">
<h5 id="orgc6fc2a3"><span class="section-number-5">3.6.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-org6bc70d5" class="outline-5">
<h5 id="org6bc70d5"><span class="section-number-5">3.6.2.2</span> Source code for default functions</h5>
<div id="outline-container-org23d194f" class="outline-5">
<h5 id="org23d194f"><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>
@ -4112,8 +4112,8 @@ This section concerns API calls related to string attributes.
</div>
</div>
<div id="outline-container-orgf559a3e" class="outline-4">
<h4 id="orgf559a3e"><span class="section-number-4">3.6.3</span> Fortran templates for front end</h4>
<div id="outline-container-org9c41a8c" class="outline-4">
<h4 id="org9c41a8c"><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.
@ -4190,8 +4190,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-org4db1c04" class="outline-4">
<h4 id="org4db1c04"><span class="section-number-4">3.6.4</span> Python templates for front end</h4>
<div id="outline-container-org7837d60" class="outline-4">
<h4 id="org7837d60"><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>:
@ -4281,8 +4281,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-orged0ae67" class="outline-2">
<h2 id="orged0ae67"><span class="section-number-2">4</span> Fortran helper/wrapper functions</h2>
<div id="outline-container-org9c14c96" class="outline-2">
<h2 id="org9c14c96"><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.
@ -4417,7 +4417,7 @@ 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: 2021-11-18 Thu 13:35</p>
<p class="date">Created: 2021-11-18 Thu 15:47</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>
<!-- 2021-11-18 Thu 13:35 -->
<!-- 2021-11-18 Thu 15:47 -->
<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="#org49ee306">1. HDF5 back end</a>
<li><a href="#orgac0a5ea">1. HDF5 back end</a>
<ul>
<li><a href="#org852fdca">1.1. Template for HDF5 definitions</a></li>
<li><a href="#orgeacd5dd">1.2. Template for HDF5 structures</a></li>
<li><a href="#org9db0bf2">1.3. Template for HDF5 init/deinit</a></li>
<li><a href="#org4005811">1.4. Template for HDF5 has/read/write the numerical attribute</a></li>
<li><a href="#orgee6a275">1.5. Template for HDF5 has/read/write the dataset of numerical data</a></li>
<li><a href="#org3d1f746">1.6. Template for HDF5 has/read/write the dataset of strings</a></li>
<li><a href="#orgaf5c58a">1.7. Template for HDF5 has/read/write the string attribute</a></li>
<li><a href="#org67d6baf">1.1. Template for HDF5 definitions</a></li>
<li><a href="#org99b28a3">1.2. Template for HDF5 structures</a></li>
<li><a href="#org7321283">1.3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgf63bcc4">1.4. Template for HDF5 has/read/write the numerical attribute</a></li>
<li><a href="#orgf2f6f81">1.5. Template for HDF5 has/read/write the dataset of numerical data</a></li>
<li><a href="#orgdf7b795">1.6. Template for HDF5 has/read/write the dataset of strings</a></li>
<li><a href="#org1216a25">1.7. Template for HDF5 has/read/write the string attribute</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org49ee306" class="outline-2">
<h2 id="org49ee306"><span class="section-number-2">1</span> HDF5 back end</h2>
<div id="outline-container-orgac0a5ea" class="outline-2">
<h2 id="orgac0a5ea"><span class="section-number-2">1</span> HDF5 back end</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-org852fdca" class="outline-3">
<h3 id="org852fdca"><span class="section-number-3">1.1</span> Template for HDF5 definitions</h3>
<div id="outline-container-org67d6baf" class="outline-3">
<h3 id="org67d6baf"><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-orgeacd5dd" class="outline-3">
<h3 id="orgeacd5dd"><span class="section-number-3">1.2</span> Template for HDF5 structures</h3>
<div id="outline-container-org99b28a3" class="outline-3">
<h3 id="org99b28a3"><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-org9db0bf2" class="outline-3">
<h3 id="org9db0bf2"><span class="section-number-3">1.3</span> Template for HDF5 init/deinit</h3>
<div id="outline-container-org7321283" class="outline-3">
<h3 id="org7321283"><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-org4005811" class="outline-3">
<h3 id="org4005811"><span class="section-number-3">1.4</span> Template for HDF5 has/read/write the numerical attribute</h3>
<div id="outline-container-orgf63bcc4" class="outline-3">
<h3 id="orgf63bcc4"><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-orgee6a275" class="outline-3">
<h3 id="orgee6a275"><span class="section-number-3">1.5</span> Template for HDF5 has/read/write the dataset of numerical data</h3>
<div id="outline-container-orgf2f6f81" class="outline-3">
<h3 id="orgf2f6f81"><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-org3d1f746" class="outline-3">
<h3 id="org3d1f746"><span class="section-number-3">1.6</span> Template for HDF5 has/read/write the dataset of strings</h3>
<div id="outline-container-orgdf7b795" class="outline-3">
<h3 id="orgdf7b795"><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-orgaf5c58a" class="outline-3">
<h3 id="orgaf5c58a"><span class="section-number-3">1.7</span> Template for HDF5 has/read/write the string attribute</h3>
<div id="outline-container-org1216a25" class="outline-3">
<h3 id="org1216a25"><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: 2021-11-18 Thu 13:35</p>
<p class="date">Created: 2021-11-18 Thu 15:47</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>
<!-- 2021-11-18 Thu 13:35 -->
<!-- 2021-11-18 Thu 15:47 -->
<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="#org29904bb">1. TEXT back end</a>
<li><a href="#orgbee9869">1. TEXT back end</a>
<ul>
<li><a href="#org1daae06">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#orgd0cab51">1.2. Template for general structure in text back end</a></li>
<li><a href="#org1d65fdd">1.3. Initialize function (constant part)</a></li>
<li><a href="#orga444414">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#org2f284a0">1.5. Template for text read struct</a></li>
<li><a href="#org7409db0">1.6. Template for text flush struct</a></li>
<li><a href="#org4df469f">1.7. Template for text free memory</a></li>
<li><a href="#org8ab29ae">1.8. Template for has/read/write the numerical attribute</a></li>
<li><a href="#orgfc5a618">1.9. Template for has/read/write the dataset of numerical data</a></li>
<li><a href="#orgec645c2">1.10. Template for has/read/write the dataset of strings</a></li>
<li><a href="#org48fbf5b">1.11. Template for has/read/write the string attribute</a></li>
<li><a href="#org00d1d85">1.12. RDM struct (hard-coded)</a>
<li><a href="#org59ac0a1">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#org3804cae">1.2. Template for general structure in text back end</a></li>
<li><a href="#org7a2b3d4">1.3. Initialize function (constant part)</a></li>
<li><a href="#orgffd6e6d">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#org6328890">1.5. Template for text read struct</a></li>
<li><a href="#orgec9ff86">1.6. Template for text flush struct</a></li>
<li><a href="#org1f2e0c2">1.7. Template for text free memory</a></li>
<li><a href="#org5ac950a">1.8. Template for has/read/write the numerical attribute</a></li>
<li><a href="#orgc997824">1.9. Template for has/read/write the dataset of numerical data</a></li>
<li><a href="#orgcca3edd">1.10. Template for has/read/write the dataset of strings</a></li>
<li><a href="#org2a65a50">1.11. Template for has/read/write the string attribute</a></li>
<li><a href="#org9ce3e20">1.12. RDM struct (hard-coded)</a>
<ul>
<li><a href="#org0970f25">1.12.1. Read the complete struct</a></li>
<li><a href="#org1f6f9d3">1.12.2. Flush the complete struct</a></li>
<li><a href="#orgc8677c2">1.12.3. Free memory</a></li>
<li><a href="#orgffff108">1.12.4. Read/Write the one<sub>e</sub> attribute</a></li>
<li><a href="#orgef258a8">1.12.5. Read/Write the two<sub>e</sub> attribute</a></li>
<li><a href="#orga664af9">1.12.1. Read the complete struct</a></li>
<li><a href="#org69f5ca3">1.12.2. Flush the complete struct</a></li>
<li><a href="#org2d53580">1.12.3. Free memory</a></li>
<li><a href="#org3acee4a">1.12.4. Read/Write the one<sub>e</sub> attribute</a></li>
<li><a href="#org1e37f2f">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-org29904bb" class="outline-2">
<h2 id="org29904bb"><span class="section-number-2">1</span> TEXT back end</h2>
<div id="outline-container-orgbee9869" class="outline-2">
<h2 id="orgbee9869"><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-org1daae06" class="outline-3">
<h3 id="org1daae06"><span class="section-number-3">1.1</span> Template for group-related structures in text back end</h3>
<div id="outline-container-org59ac0a1" class="outline-3">
<h3 id="org59ac0a1"><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-orgd0cab51" class="outline-3">
<h3 id="orgd0cab51"><span class="section-number-3">1.2</span> Template for general structure in text back end</h3>
<div id="outline-container-org3804cae" class="outline-3">
<h3 id="org3804cae"><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-org1d65fdd" class="outline-3">
<h3 id="org1d65fdd"><span class="section-number-3">1.3</span> Initialize function (constant part)</h3>
<div id="outline-container-org7a2b3d4" class="outline-3">
<h3 id="org7a2b3d4"><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-orga444414" class="outline-3">
<h3 id="orga444414"><span class="section-number-3">1.4</span> Deinitialize function (templated part)</h3>
<div id="outline-container-orgffd6e6d" class="outline-3">
<h3 id="orgffd6e6d"><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-org2f284a0" class="outline-3">
<h3 id="org2f284a0"><span class="section-number-3">1.5</span> Template for text read struct</h3>
<div id="outline-container-org6328890" class="outline-3">
<h3 id="org6328890"><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-org7409db0" class="outline-3">
<h3 id="org7409db0"><span class="section-number-3">1.6</span> Template for text flush struct</h3>
<div id="outline-container-orgec9ff86" class="outline-3">
<h3 id="orgec9ff86"><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-org4df469f" class="outline-3">
<h3 id="org4df469f"><span class="section-number-3">1.7</span> Template for text free memory</h3>
<div id="outline-container-org1f2e0c2" class="outline-3">
<h3 id="org1f2e0c2"><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-org8ab29ae" class="outline-3">
<h3 id="org8ab29ae"><span class="section-number-3">1.8</span> Template for has/read/write the numerical attribute</h3>
<div id="outline-container-org5ac950a" class="outline-3">
<h3 id="org5ac950a"><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-orgfc5a618" class="outline-3">
<h3 id="orgfc5a618"><span class="section-number-3">1.9</span> Template for has/read/write the dataset of numerical data</h3>
<div id="outline-container-orgc997824" class="outline-3">
<h3 id="orgc997824"><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-orgec645c2" class="outline-3">
<h3 id="orgec645c2"><span class="section-number-3">1.10</span> Template for has/read/write the dataset of strings</h3>
<div id="outline-container-orgcca3edd" class="outline-3">
<h3 id="orgcca3edd"><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-org48fbf5b" class="outline-3">
<h3 id="org48fbf5b"><span class="section-number-3">1.11</span> Template for has/read/write the string attribute</h3>
<div id="outline-container-org2a65a50" class="outline-3">
<h3 id="org2a65a50"><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-org00d1d85" class="outline-3">
<h3 id="org00d1d85"><span class="section-number-3">1.12</span> RDM struct (hard-coded)</h3>
<div id="outline-container-org9ce3e20" class="outline-3">
<h3 id="org9ce3e20"><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-org0970f25" class="outline-4">
<h4 id="org0970f25"><span class="section-number-4">1.12.1</span> Read the complete struct</h4>
<div id="outline-container-orga664af9" class="outline-4">
<h4 id="orga664af9"><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-org1f6f9d3" class="outline-4">
<h4 id="org1f6f9d3"><span class="section-number-4">1.12.2</span> Flush the complete struct</h4>
<div id="outline-container-org69f5ca3" class="outline-4">
<h4 id="org69f5ca3"><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-orgc8677c2" class="outline-4">
<h4 id="orgc8677c2"><span class="section-number-4">1.12.3</span> Free memory</h4>
<div id="outline-container-org2d53580" class="outline-4">
<h4 id="org2d53580"><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-orgffff108" class="outline-4">
<h4 id="orgffff108"><span class="section-number-4">1.12.4</span> Read/Write the one<sub>e</sub> attribute</h4>
<div id="outline-container-org3acee4a" class="outline-4">
<h4 id="org3acee4a"><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-orgef258a8" class="outline-4">
<h4 id="orgef258a8"><span class="section-number-4">1.12.5</span> Read/Write the two<sub>e</sub> attribute</h4>
<div id="outline-container-org1e37f2f" class="outline-4">
<h4 id="org1e37f2f"><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: 2021-11-18 Thu 13:35</p>
<p class="date">Created: 2021-11-18 Thu 15:47</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

116
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>
<!-- 2021-11-18 Thu 13:35 -->
<!-- 2021-11-18 Thu 15:47 -->
<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="#orga60d977">1. Metadata (metadata group)</a></li>
<li><a href="#org5af70b7">2. Electron (electron group)</a></li>
<li><a href="#org8a1f003">3. Nucleus (nucleus group)</a></li>
<li><a href="#org2c65ce1">4. Effective core potentials (ecp group)</a>
<li><a href="#orgf4e6e33">1. Metadata (metadata group)</a></li>
<li><a href="#org321fc0e">2. Electron (electron group)</a></li>
<li><a href="#orga74fdcb">3. Nucleus (nucleus group)</a></li>
<li><a href="#orge92a0ad">4. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org036856e">4.1. Example</a></li>
<li><a href="#orgad5aa5f">4.1. Example</a></li>
</ul>
</li>
<li><a href="#org4d2d6f7">5. Basis set (basis group)</a>
<li><a href="#org58842fa">5. Basis set (basis group)</a>
<ul>
<li><a href="#orgac93d3f">5.1. Example</a></li>
<li><a href="#org1641791">5.1. Example</a></li>
</ul>
</li>
<li><a href="#org112ab53">6. Atomic orbitals (ao group)</a>
<li><a href="#org1e55b33">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="#org682b6be">7. Molecular orbitals (mo group)</a>
<li><a href="#orgb125b38">7. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org391cc5e">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgd48d8cd">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org8b0b618">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org2b72a08">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#org28c9343">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#orgb814863">9. <span class="todo TODO">TODO</span> Reduced density matrices (rdm group)</a></li>
<li><a href="#org481e582">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#orge582e07">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-orga60d977" class="outline-2">
<h2 id="orga60d977"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-orgf4e6e33" class="outline-2">
<h2 id="orgf4e6e33"><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="org244fe86" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org12cfca3" 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-org5af70b7" class="outline-2">
<h2 id="org5af70b7"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div id="outline-container-org321fc0e" class="outline-2">
<h2 id="org321fc0e"><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="org93d3510" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org254205c" 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-org8a1f003" class="outline-2">
<h2 id="org8a1f003"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div id="outline-container-orga74fdcb" class="outline-2">
<h2 id="orga74fdcb"><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="org66d53a0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga5491f0" 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-org2c65ce1" class="outline-2">
<h2 id="org2c65ce1"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div id="outline-container-orge92a0ad" class="outline-2">
<h2 id="orge92a0ad"><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="org9c04814" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org6cabf11" 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-org036856e" class="outline-3">
<h3 id="org036856e"><span class="section-number-3">4.1</span> Example</h3>
<div id="outline-container-orgad5aa5f" class="outline-3">
<h3 id="orgad5aa5f"><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
@ -788,8 +788,8 @@ power = [
</div>
</div>
<div id="outline-container-org4d2d6f7" class="outline-2">
<h2 id="org4d2d6f7"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div id="outline-container-org58842fa" class="outline-2">
<h2 id="org58842fa"><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="orgfad5aba" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2319c40" 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-orgac93d3f" class="outline-3">
<h3 id="orgac93d3f"><span class="section-number-3">5.1</span> Example</h3>
<div id="outline-container-org1641791" class="outline-3">
<h3 id="org1641791"><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-org112ab53" class="outline-2">
<h2 id="org112ab53"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div id="outline-container-org1e55b33" class="outline-2">
<h2 id="org1e55b33"><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="#org4d2d6f7">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#org58842fa">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="orgcbe818f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org6a22d5a" 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-orgba9b087" class="outline-3">
<h3 id="ao_one_e"><a id="orgba9b087"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div id="outline-container-org9003f6f" class="outline-3">
<h3 id="ao_one_e"><a id="org9003f6f"></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="orgb7db77d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org40e458c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1208,8 +1208,8 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org8a083a9" class="outline-3">
<h3 id="ao_two_e"><a id="org8a083a9"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div id="outline-container-org891da4c" class="outline-3">
<h3 id="ao_two_e"><a id="org891da4c"></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="orgb5c9e93" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org6edc09a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1270,10 +1270,10 @@ notation.
</div>
</div>
<div id="outline-container-org682b6be" class="outline-2">
<h2 id="org682b6be"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div id="outline-container-orgb125b38" class="outline-2">
<h2 id="orgb125b38"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
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@ -1339,8 +1339,8 @@ notation.
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<h3 id="org391cc5e"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
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<h3 id="org8b0b618"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
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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.
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@ -1415,8 +1415,8 @@ the basis of molecular orbitals.
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<h3 id="orgd48d8cd"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
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<h3 id="org2b72a08"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
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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.
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@ -1464,13 +1464,13 @@ the basis of molecular orbitals.
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<h2 id="org28c9343"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
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<h2 id="org481e582"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
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<h2 id="orgb814863"><span class="section-number-2">9</span> <span class="todo TODO">TODO</span> Reduced density matrices (rdm group)</h2>
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<h2 id="orge582e07"><span class="section-number-2">9</span> <span class="todo TODO">TODO</span> Reduced density matrices (rdm group)</h2>
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@ -1525,7 +1525,7 @@ the basis of molecular orbitals.
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<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2021-11-18 Thu 13:35</p>
<p class="date">Created: 2021-11-18 Thu 15:47</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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