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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>
<!-- 2021-11-02 Tue 15:29 -->
<!-- 2021-11-02 Tue 20:53 -->
<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: 2021-11-02 Tue 15:29</p>
<p class="date">Created: 2021-11-02 Tue 20:53</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>
<!-- 2021-11-02 Tue 15:29 -->
<!-- 2021-11-02 Tue 20:53 -->
<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="#org2498faa">1. Text back end</a></li>
<li><a href="#orge738bb9">2. HDF5 Back end</a></li>
<li><a href="#org9dfe786">1. Text back end</a></li>
<li><a href="#org8d498dd">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-org2498faa" class="outline-2">
<h2 id="org2498faa"><span class="section-number-2">1</span> Text back end</h2>
<div id="outline-container-org9dfe786" class="outline-2">
<h2 id="org9dfe786"><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-orge738bb9" class="outline-2">
<h2 id="orge738bb9"><span class="section-number-2">2</span> HDF5 Back end</h2>
<div id="outline-container-org8d498dd" class="outline-2">
<h2 id="org8d498dd"><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: 2021-11-02 Tue 15:29</p>
<p class="date">Created: 2021-11-02 Tue 20:53</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>
<!-- 2021-11-02 Tue 15:29 -->
<!-- 2021-11-02 Tue 20:53 -->
<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: 2021-11-02 Tue 15:29</p>
<p class="date">Created: 2021-11-02 Tue 20:53</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>
<!-- 2021-11-02 Tue 15:29 -->
<!-- 2021-11-02 Tue 20:53 -->
<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="#org12af372">1. Coding conventions</a>
<li><a href="#org3ecc36f">1. Coding conventions</a>
<ul>
<li><a href="#org9cb8743">1.1. Memory allocation</a></li>
<li><a href="#org171f541">1.1. Memory allocation</a></li>
</ul>
</li>
<li><a href="#orge0baa5e">2. Front end</a>
<li><a href="#org3650871">2. Front end</a>
<ul>
<li><a href="#org4463812">2.1. Error handling</a>
<li><a href="#org0771e31">2.1. Error handling</a>
<ul>
<li><a href="#org26a0815">2.1.1. Decoding errors</a>
<li><a href="#org2457096">2.1.1. Decoding errors</a>
<ul>
<li><a href="#orgf3c3dd4">2.1.1.1. C source code</a></li>
<li><a href="#org1ceaed7">2.1.1.2. Fortran interface</a></li>
<li><a href="#orgacf9219">2.1.1.3. Python interface</a></li>
<li><a href="#org4b5879e">2.1.1.1. C source code</a></li>
<li><a href="#org19fd21b">2.1.1.2. Fortran interface</a></li>
<li><a href="#orga02bfb0">2.1.1.3. Python interface</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org33b595b">2.2. Back ends</a>
<li><a href="#orged3002f">2.2. Back ends</a>
<ul>
<li><a href="#orgda64cd4">2.2.1. C</a></li>
<li><a href="#orgbde1885">2.2.2. Fortran</a></li>
<li><a href="#org83b3249">2.2.3. Python</a></li>
<li><a href="#orge634257">2.2.1. C</a></li>
<li><a href="#orgdc2ae9a">2.2.2. Fortran</a></li>
<li><a href="#orgd03832b">2.2.3. Python</a></li>
</ul>
</li>
<li><a href="#org5081bc4">2.3. Read/write behavior</a></li>
<li><a href="#org076c4f7">2.4. TREXIO file type</a>
<li><a href="#orgcc5a1f1">2.3. Read/write behavior</a></li>
<li><a href="#org44cfb9c">2.4. TREXIO file type</a>
<ul>
<li><a href="#org5e4df8f">2.4.1. TREXIO<sub>File</sub> Python class</a></li>
<li><a href="#org64f2df6">2.4.1. TREXIO<sub>File</sub> Python class</a></li>
</ul>
</li>
<li><a href="#org92525bc">2.5. Polymorphism of the file handle</a></li>
<li><a href="#orgcd7456e">2.6. File opening</a>
<li><a href="#orge1bd46d">2.5. Polymorphism of the file handle</a></li>
<li><a href="#orgb798019">2.6. File opening</a>
<ul>
<li><a href="#orgb146a21">2.6.1. C</a></li>
<li><a href="#org29e9049">2.6.2. Fortran</a></li>
<li><a href="#org28387bb">2.6.3. Python</a></li>
<li><a href="#orgeb20831">2.6.4. Zero-based versus one-based arrays of indices</a></li>
<li><a href="#org031b799">2.6.1. C</a></li>
<li><a href="#org5825ea2">2.6.2. Fortran</a></li>
<li><a href="#org5d859b3">2.6.3. Python</a></li>
<li><a href="#org357ea23">2.6.4. Zero-based versus one-based arrays of indices</a></li>
</ul>
</li>
<li><a href="#org9e1e656">2.7. File closing</a>
<li><a href="#orgbfef165">2.7. File closing</a>
<ul>
<li><a href="#org56c0a04">2.7.1. C</a></li>
<li><a href="#org32df511">2.7.2. Fortran</a></li>
<li><a href="#org96cadc1">2.7.3. Python</a></li>
<li><a href="#org238381c">2.7.1. C</a></li>
<li><a href="#orgc38d59f">2.7.2. Fortran</a></li>
<li><a href="#orgd861992">2.7.3. Python</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgbc755f6">3. Templates for front end</a>
<li><a href="#orgbf5bef7">3. Templates for front end</a>
<ul>
<li><a href="#orgec6054d">3.1. Description</a></li>
<li><a href="#org9c44d7e">3.2. Templates for front end has/read/write a single numerical attribute</a>
<li><a href="#org027dca3">3.1. Description</a></li>
<li><a href="#org1fa2fcf">3.2. Templates for front end has/read/write a single numerical attribute</a>
<ul>
<li><a href="#org74d9f02">3.2.1. Introduction</a></li>
<li><a href="#org683ebdd">3.2.2. C templates for front end</a>
<li><a href="#org2a71620">3.2.1. Introduction</a></li>
<li><a href="#org875401d">3.2.2. C templates for front end</a>
<ul>
<li><a href="#org7bd40ee">3.2.2.1. Function declarations</a></li>
<li><a href="#org0ee4a22">3.2.2.2. Source code for double precision functions</a></li>
<li><a href="#orgda36451">3.2.2.3. Source code for single precision functions</a></li>
<li><a href="#orgb5edd15">3.2.2.4. Source code for default functions</a></li>
<li><a href="#org98b2f60">3.2.2.1. Function declarations</a></li>
<li><a href="#orga2bff69">3.2.2.2. Source code for double precision functions</a></li>
<li><a href="#org9a961e2">3.2.2.3. Source code for single precision functions</a></li>
<li><a href="#org7e328bb">3.2.2.4. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#org225d338">3.2.3. Fortran templates for front end</a></li>
<li><a href="#org784bad1">3.2.4. Python templates for front end</a></li>
<li><a href="#org56ab3f4">3.2.3. Fortran templates for front end</a></li>
<li><a href="#orgd09449d">3.2.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#orgeae98af">3.3. Templates for front end has/read/write a dataset of numerical data</a>
<li><a href="#org982e713">3.3. Templates for front end has/read/write a dataset of numerical data</a>
<ul>
<li><a href="#org55c51d1">3.3.1. Introduction</a></li>
<li><a href="#org6f27bda">3.3.2. C templates for front end</a>
<li><a href="#org9381a80">3.3.1. Introduction</a></li>
<li><a href="#org2de9d8a">3.3.2. C templates for front end</a>
<ul>
<li><a href="#org81509fa">3.3.2.1. Function declarations</a></li>
<li><a href="#orgce613d9">3.3.2.2. Source code for double precision functions</a></li>
<li><a href="#orgb44a5d9">3.3.2.3. Source code for single precision functions</a></li>
<li><a href="#org4b22efc">3.3.2.4. Source code for memory-safe functions</a></li>
<li><a href="#org062c688">3.3.2.5. Source code for default functions</a></li>
<li><a href="#org1a5d430">3.3.2.1. Function declarations</a></li>
<li><a href="#orgffd4ba4">3.3.2.2. Source code for double precision functions</a></li>
<li><a href="#orgf2cc0e8">3.3.2.3. Source code for single precision functions</a></li>
<li><a href="#org5afe45e">3.3.2.4. Source code for memory-safe functions</a></li>
<li><a href="#org7207121">3.3.2.5. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#orgfc07011">3.3.3. Fortran templates for front end</a></li>
<li><a href="#org95a19d2">3.3.4. Python templates for front end</a></li>
<li><a href="#org88d5c91">3.3.3. Fortran templates for front end</a></li>
<li><a href="#org656dbab">3.3.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#org73ae3dc">3.4. Sparse data structures</a></li>
<li><a href="#orga4e95fb">3.5. Templates for front end has/read/write a dataset of strings</a>
<li><a href="#orgad4e335">3.4. Sparse data structures</a></li>
<li><a href="#orgb0b443b">3.5. Templates for front end has/read/write a dataset of strings</a>
<ul>
<li><a href="#orgff362d5">3.5.1. Introduction</a></li>
<li><a href="#orge850807">3.5.2. C templates for front end</a>
<li><a href="#org9f2d4b6">3.5.1. Introduction</a></li>
<li><a href="#org8cac5c4">3.5.2. C templates for front end</a>
<ul>
<li><a href="#org92ac8ae">3.5.2.1. Function declarations</a></li>
<li><a href="#orgf25541d">3.5.2.2. Source code for default functions</a></li>
<li><a href="#org681d869">3.5.2.1. Function declarations</a></li>
<li><a href="#org156a73e">3.5.2.2. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#org50ddc57">3.5.3. Fortran templates for front end</a></li>
<li><a href="#orgc9a9a99">3.5.4. Python templates for front end</a></li>
<li><a href="#orgf65ca22">3.5.3. Fortran templates for front end</a></li>
<li><a href="#org1d3c69f">3.5.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#org52a769e">3.6. Templates for front end has/read/write a single string attribute</a>
<li><a href="#org7afb746">3.6. Templates for front end has/read/write a single string attribute</a>
<ul>
<li><a href="#org523c33d">3.6.1. Introduction</a></li>
<li><a href="#org75991c7">3.6.2. C templates for front end</a>
<li><a href="#org36ba796">3.6.1. Introduction</a></li>
<li><a href="#orgd7c67f9">3.6.2. C templates for front end</a>
<ul>
<li><a href="#org81b1d3e">3.6.2.1. Function declarations</a></li>
<li><a href="#org04545ed">3.6.2.2. Source code for default functions</a></li>
<li><a href="#org6c8c47f">3.6.2.1. Function declarations</a></li>
<li><a href="#org989bf28">3.6.2.2. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#org47f63df">3.6.3. Fortran templates for front end</a></li>
<li><a href="#orgd42dd7b">3.6.4. Python templates for front end</a></li>
<li><a href="#org233044b">3.6.3. Fortran templates for front end</a></li>
<li><a href="#org1480185">3.6.4. Python templates for front end</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org471e2fa">4. Fortran helper/wrapper functions</a></li>
<li><a href="#orga120c89">4. Fortran helper/wrapper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-org12af372" class="outline-2">
<h2 id="org12af372"><span class="section-number-2">1</span> Coding conventions</h2>
<div id="outline-container-org3ecc36f" class="outline-2">
<h2 id="org3ecc36f"><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-org9cb8743" class="outline-3">
<h3 id="org9cb8743"><span class="section-number-3">1.1</span> Memory allocation</h3>
<div id="outline-container-org171f541" class="outline-3">
<h3 id="org171f541"><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-orge0baa5e" class="outline-2">
<h2 id="orge0baa5e"><span class="section-number-2">2</span> Front end</h2>
<div id="outline-container-org3650871" class="outline-2">
<h2 id="org3650871"><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-org4463812" class="outline-3">
<h3 id="org4463812"><span class="section-number-3">2.1</span> Error handling</h3>
<div id="outline-container-org0771e31" class="outline-3">
<h3 id="org0771e31"><span class="section-number-3">2.1</span> Error handling</h3>
<div class="outline-text-3" id="text-2-1">
<table id="org75c810c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgda715c3" 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-org26a0815" class="outline-4">
<h4 id="org26a0815"><span class="section-number-4">2.1.1</span> Decoding errors</h4>
<div id="outline-container-org2457096" class="outline-4">
<h4 id="org2457096"><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-orgf3c3dd4" class="outline-5">
<h5 id="orgf3c3dd4"><span class="section-number-5">2.1.1.1</span> C source code</h5>
<div id="outline-container-org4b5879e" class="outline-5">
<h5 id="org4b5879e"><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-org1ceaed7" class="outline-5">
<h5 id="org1ceaed7"><span class="section-number-5">2.1.1.2</span> Fortran interface</h5>
<div id="outline-container-org19fd21b" class="outline-5">
<h5 id="org19fd21b"><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-orgacf9219" class="outline-5">
<h5 id="orgacf9219"><span class="section-number-5">2.1.1.3</span> Python interface</h5>
<div id="outline-container-orga02bfb0" class="outline-5">
<h5 id="orga02bfb0"><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-org33b595b" class="outline-3">
<h3 id="org33b595b"><span class="section-number-3">2.2</span> Back ends</h3>
<div id="outline-container-orged3002f" class="outline-3">
<h3 id="orged3002f"><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-orgda64cd4" class="outline-4">
<h4 id="orgda64cd4"><span class="section-number-4">2.2.1</span> C</h4>
<div id="outline-container-orge634257" class="outline-4">
<h4 id="orge634257"><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-orgbde1885" class="outline-4">
<h4 id="orgbde1885"><span class="section-number-4">2.2.2</span> Fortran</h4>
<div id="outline-container-orgdc2ae9a" class="outline-4">
<h4 id="orgdc2ae9a"><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-org83b3249" class="outline-4">
<h4 id="org83b3249"><span class="section-number-4">2.2.3</span> Python</h4>
<div id="outline-container-orgd03832b" class="outline-4">
<h4 id="orgd03832b"><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-org5081bc4" class="outline-3">
<h3 id="org5081bc4"><span class="section-number-3">2.3</span> Read/write behavior</h3>
<div id="outline-container-orgcc5a1f1" class="outline-3">
<h3 id="orgcc5a1f1"><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-org076c4f7" class="outline-3">
<h3 id="org076c4f7"><span class="section-number-3">2.4</span> TREXIO file type</h3>
<div id="outline-container-org44cfb9c" class="outline-3">
<h3 id="org44cfb9c"><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-org5e4df8f" class="outline-4">
<h4 id="org5e4df8f"><span class="section-number-4">2.4.1</span> TREXIO<sub>File</sub> Python class</h4>
<div id="outline-container-org64f2df6" class="outline-4">
<h4 id="org64f2df6"><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-org92525bc" class="outline-3">
<h3 id="org92525bc"><span class="section-number-3">2.5</span> Polymorphism of the file handle</h3>
<div id="outline-container-orge1bd46d" class="outline-3">
<h3 id="orge1bd46d"><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-orgcd7456e" class="outline-3">
<h3 id="orgcd7456e"><span class="section-number-3">2.6</span> File opening</h3>
<div id="outline-container-orgb798019" class="outline-3">
<h3 id="orgb798019"><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-orgb146a21" class="outline-4">
<h4 id="orgb146a21"><span class="section-number-4">2.6.1</span> C</h4>
<div id="outline-container-org031b799" class="outline-4">
<h4 id="org031b799"><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-org29e9049" class="outline-4">
<h4 id="org29e9049"><span class="section-number-4">2.6.2</span> Fortran</h4>
<div id="outline-container-org5825ea2" class="outline-4">
<h4 id="org5825ea2"><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-org28387bb" class="outline-4">
<h4 id="org28387bb"><span class="section-number-4">2.6.3</span> Python</h4>
<div id="outline-container-org5d859b3" class="outline-4">
<h4 id="org5d859b3"><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-orgeb20831" class="outline-4">
<h4 id="orgeb20831"><span class="section-number-4">2.6.4</span> Zero-based versus one-based arrays of indices</h4>
<div id="outline-container-org357ea23" class="outline-4">
<h4 id="org357ea23"><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-org9e1e656" class="outline-3">
<h3 id="org9e1e656"><span class="section-number-3">2.7</span> File closing</h3>
<div id="outline-container-orgbfef165" class="outline-3">
<h3 id="orgbfef165"><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-org56c0a04" class="outline-4">
<h4 id="org56c0a04"><span class="section-number-4">2.7.1</span> C</h4>
<div id="outline-container-org238381c" class="outline-4">
<h4 id="org238381c"><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-org32df511" class="outline-4">
<h4 id="org32df511"><span class="section-number-4">2.7.2</span> Fortran</h4>
<div id="outline-container-orgc38d59f" class="outline-4">
<h4 id="orgc38d59f"><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-org96cadc1" class="outline-4">
<h4 id="org96cadc1"><span class="section-number-4">2.7.3</span> Python</h4>
<div id="outline-container-orgd861992" class="outline-4">
<h4 id="orgd861992"><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-orgbc755f6" class="outline-2">
<h2 id="orgbc755f6"><span class="section-number-2">3</span> Templates for front end</h2>
<div id="outline-container-orgbf5bef7" class="outline-2">
<h2 id="orgbf5bef7"><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-orgec6054d" class="outline-3">
<h3 id="orgec6054d"><span class="section-number-3">3.1</span> Description</h3>
<div id="outline-container-org027dca3" class="outline-3">
<h3 id="org027dca3"><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-org9c44d7e" class="outline-3">
<h3 id="org9c44d7e"><span class="section-number-3">3.2</span> Templates for front end has/read/write a single numerical attribute</h3>
<div id="outline-container-org1fa2fcf" class="outline-3">
<h3 id="org1fa2fcf"><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-org74d9f02" class="outline-4">
<h4 id="org74d9f02"><span class="section-number-4">3.2.1</span> Introduction</h4>
<div id="outline-container-org2a71620" class="outline-4">
<h4 id="org2a71620"><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-org683ebdd" class="outline-4">
<h4 id="org683ebdd"><span class="section-number-4">3.2.2</span> C templates for front end</h4>
<div id="outline-container-org875401d" class="outline-4">
<h4 id="org875401d"><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-org7bd40ee" class="outline-5">
<h5 id="org7bd40ee"><span class="section-number-5">3.2.2.1</span> Function declarations</h5>
<div id="outline-container-org98b2f60" class="outline-5">
<h5 id="org98b2f60"><span class="section-number-5">3.2.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-org0ee4a22" class="outline-5">
<h5 id="org0ee4a22"><span class="section-number-5">3.2.2.2</span> Source code for double precision functions</h5>
<div id="outline-container-orga2bff69" class="outline-5">
<h5 id="orga2bff69"><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-orgda36451" class="outline-5">
<h5 id="orgda36451"><span class="section-number-5">3.2.2.3</span> Source code for single precision functions</h5>
<div id="outline-container-org9a961e2" class="outline-5">
<h5 id="org9a961e2"><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-orgb5edd15" class="outline-5">
<h5 id="orgb5edd15"><span class="section-number-5">3.2.2.4</span> Source code for default functions</h5>
<div id="outline-container-org7e328bb" class="outline-5">
<h5 id="org7e328bb"><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-org225d338" class="outline-4">
<h4 id="org225d338"><span class="section-number-4">3.2.3</span> Fortran templates for front end</h4>
<div id="outline-container-org56ab3f4" class="outline-4">
<h4 id="org56ab3f4"><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-org784bad1" class="outline-4">
<h4 id="org784bad1"><span class="section-number-4">3.2.4</span> Python templates for front end</h4>
<div id="outline-container-orgd09449d" class="outline-4">
<h4 id="orgd09449d"><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-orgeae98af" class="outline-3">
<h3 id="orgeae98af"><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-org982e713" class="outline-3">
<h3 id="org982e713"><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-org55c51d1" class="outline-4">
<h4 id="org55c51d1"><span class="section-number-4">3.3.1</span> Introduction</h4>
<div id="outline-container-org9381a80" class="outline-4">
<h4 id="org9381a80"><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-org6f27bda" class="outline-4">
<h4 id="org6f27bda"><span class="section-number-4">3.3.2</span> C templates for front end</h4>
<div id="outline-container-org2de9d8a" class="outline-4">
<h4 id="org2de9d8a"><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-org81509fa" class="outline-5">
<h5 id="org81509fa"><span class="section-number-5">3.3.2.1</span> Function declarations</h5>
<div id="outline-container-org1a5d430" class="outline-5">
<h5 id="org1a5d430"><span class="section-number-5">3.3.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-orgce613d9" class="outline-5">
<h5 id="orgce613d9"><span class="section-number-5">3.3.2.2</span> Source code for double precision functions</h5>
<div id="outline-container-orgffd4ba4" class="outline-5">
<h5 id="orgffd4ba4"><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-orgb44a5d9" class="outline-5">
<h5 id="orgb44a5d9"><span class="section-number-5">3.3.2.3</span> Source code for single precision functions</h5>
<div id="outline-container-orgf2cc0e8" class="outline-5">
<h5 id="orgf2cc0e8"><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-org4b22efc" class="outline-5">
<h5 id="org4b22efc"><span class="section-number-5">3.3.2.4</span> Source code for memory-safe functions</h5>
<div id="outline-container-org5afe45e" class="outline-5">
<h5 id="org5afe45e"><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="orge222aad"><span style="color: #228b22;">trexio_exit_code</span> <span style="color: #a0522d;">rc</span>;
<pre class="src src-c" id="org26882d9"><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-org062c688" class="outline-5">
<h5 id="org062c688"><span class="section-number-5">3.3.2.5</span> Source code for default functions</h5>
<div id="outline-container-org7207121" class="outline-5">
<h5 id="org7207121"><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-orgfc07011" class="outline-4">
<h4 id="orgfc07011"><span class="section-number-4">3.3.3</span> Fortran templates for front end</h4>
<div id="outline-container-org88d5c91" class="outline-4">
<h4 id="org88d5c91"><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-org95a19d2" class="outline-4">
<h4 id="org95a19d2"><span class="section-number-4">3.3.4</span> Python templates for front end</h4>
<div id="outline-container-org656dbab" class="outline-4">
<h4 id="org656dbab"><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-org73ae3dc" class="outline-3">
<h3 id="org73ae3dc"><span class="section-number-3">3.4</span> Sparse data structures</h3>
<div id="outline-container-orgad4e335" class="outline-3">
<h3 id="orgad4e335"><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-orga4e95fb" class="outline-3">
<h3 id="orga4e95fb"><span class="section-number-3">3.5</span> Templates for front end has/read/write a dataset of strings</h3>
<div id="outline-container-orgb0b443b" class="outline-3">
<h3 id="orgb0b443b"><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-orgff362d5" class="outline-4">
<h4 id="orgff362d5"><span class="section-number-4">3.5.1</span> Introduction</h4>
<div id="outline-container-org9f2d4b6" class="outline-4">
<h4 id="org9f2d4b6"><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-orge850807" class="outline-4">
<h4 id="orge850807"><span class="section-number-4">3.5.2</span> C templates for front end</h4>
<div id="outline-container-org8cac5c4" class="outline-4">
<h4 id="org8cac5c4"><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-org92ac8ae" class="outline-5">
<h5 id="org92ac8ae"><span class="section-number-5">3.5.2.1</span> Function declarations</h5>
<div id="outline-container-org681d869" class="outline-5">
<h5 id="org681d869"><span class="section-number-5">3.5.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-orgf25541d" class="outline-5">
<h5 id="orgf25541d"><span class="section-number-5">3.5.2.2</span> Source code for default functions</h5>
<div id="outline-container-org156a73e" class="outline-5">
<h5 id="org156a73e"><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-org50ddc57" class="outline-4">
<h4 id="org50ddc57"><span class="section-number-4">3.5.3</span> Fortran templates for front end</h4>
<div id="outline-container-orgf65ca22" class="outline-4">
<h4 id="orgf65ca22"><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-orgc9a9a99" class="outline-4">
<h4 id="orgc9a9a99"><span class="section-number-4">3.5.4</span> Python templates for front end</h4>
<div id="outline-container-org1d3c69f" class="outline-4">
<h4 id="org1d3c69f"><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-org52a769e" class="outline-3">
<h3 id="org52a769e"><span class="section-number-3">3.6</span> Templates for front end has/read/write a single string attribute</h3>
<div id="outline-container-org7afb746" class="outline-3">
<h3 id="org7afb746"><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-org523c33d" class="outline-4">
<h4 id="org523c33d"><span class="section-number-4">3.6.1</span> Introduction</h4>
<div id="outline-container-org36ba796" class="outline-4">
<h4 id="org36ba796"><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-org75991c7" class="outline-4">
<h4 id="org75991c7"><span class="section-number-4">3.6.2</span> C templates for front end</h4>
<div id="outline-container-orgd7c67f9" class="outline-4">
<h4 id="orgd7c67f9"><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-org81b1d3e" class="outline-5">
<h5 id="org81b1d3e"><span class="section-number-5">3.6.2.1</span> Function declarations</h5>
<div id="outline-container-org6c8c47f" class="outline-5">
<h5 id="org6c8c47f"><span class="section-number-5">3.6.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-org04545ed" class="outline-5">
<h5 id="org04545ed"><span class="section-number-5">3.6.2.2</span> Source code for default functions</h5>
<div id="outline-container-org989bf28" class="outline-5">
<h5 id="org989bf28"><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-org47f63df" class="outline-4">
<h4 id="org47f63df"><span class="section-number-4">3.6.3</span> Fortran templates for front end</h4>
<div id="outline-container-org233044b" class="outline-4">
<h4 id="org233044b"><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-orgd42dd7b" class="outline-4">
<h4 id="orgd42dd7b"><span class="section-number-4">3.6.4</span> Python templates for front end</h4>
<div id="outline-container-org1480185" class="outline-4">
<h4 id="org1480185"><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-org471e2fa" class="outline-2">
<h2 id="org471e2fa"><span class="section-number-2">4</span> Fortran helper/wrapper functions</h2>
<div id="outline-container-orga120c89" class="outline-2">
<h2 id="orga120c89"><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: 2021-11-02 Tue 15:29</p>
<p class="date">Created: 2021-11-02 Tue 20:53</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>
<!-- 2021-11-02 Tue 15:29 -->
<!-- 2021-11-02 Tue 20:53 -->
<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="#orgc4590bb">1. HDF5 back end</a>
<li><a href="#orge11c2ec">1. HDF5 back end</a>
<ul>
<li><a href="#orgab9bdb4">1.1. Template for HDF5 definitions</a></li>
<li><a href="#org280258d">1.2. Template for HDF5 structures</a></li>
<li><a href="#org21ffdec">1.3. Template for HDF5 init/deinit</a></li>
<li><a href="#org9b3547c">1.4. Template for HDF5 has/read/write the numerical attribute</a></li>
<li><a href="#orgfab7c19">1.5. Template for HDF5 has/read/write the dataset of numerical data</a></li>
<li><a href="#orgeba9251">1.6. Template for HDF5 has/read/write the dataset of strings</a></li>
<li><a href="#orgac8b7d7">1.7. Template for HDF5 has/read/write the string attribute</a></li>
<li><a href="#orgad5c191">1.1. Template for HDF5 definitions</a></li>
<li><a href="#org1ba2497">1.2. Template for HDF5 structures</a></li>
<li><a href="#orgc4e0b06">1.3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgf4a49c3">1.4. Template for HDF5 has/read/write the numerical attribute</a></li>
<li><a href="#org7e90bb6">1.5. Template for HDF5 has/read/write the dataset of numerical data</a></li>
<li><a href="#org682c748">1.6. Template for HDF5 has/read/write the dataset of strings</a></li>
<li><a href="#org53326b9">1.7. Template for HDF5 has/read/write the string attribute</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-orgc4590bb" class="outline-2">
<h2 id="orgc4590bb"><span class="section-number-2">1</span> HDF5 back end</h2>
<div id="outline-container-orge11c2ec" class="outline-2">
<h2 id="orge11c2ec"><span class="section-number-2">1</span> HDF5 back end</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-orgab9bdb4" class="outline-3">
<h3 id="orgab9bdb4"><span class="section-number-3">1.1</span> Template for HDF5 definitions</h3>
<div id="outline-container-orgad5c191" class="outline-3">
<h3 id="orgad5c191"><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-org280258d" class="outline-3">
<h3 id="org280258d"><span class="section-number-3">1.2</span> Template for HDF5 structures</h3>
<div id="outline-container-org1ba2497" class="outline-3">
<h3 id="org1ba2497"><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-org21ffdec" class="outline-3">
<h3 id="org21ffdec"><span class="section-number-3">1.3</span> Template for HDF5 init/deinit</h3>
<div id="outline-container-orgc4e0b06" class="outline-3">
<h3 id="orgc4e0b06"><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-org9b3547c" class="outline-3">
<h3 id="org9b3547c"><span class="section-number-3">1.4</span> Template for HDF5 has/read/write the numerical attribute</h3>
<div id="outline-container-orgf4a49c3" class="outline-3">
<h3 id="orgf4a49c3"><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-orgfab7c19" class="outline-3">
<h3 id="orgfab7c19"><span class="section-number-3">1.5</span> Template for HDF5 has/read/write the dataset of numerical data</h3>
<div id="outline-container-org7e90bb6" class="outline-3">
<h3 id="org7e90bb6"><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-orgeba9251" class="outline-3">
<h3 id="orgeba9251"><span class="section-number-3">1.6</span> Template for HDF5 has/read/write the dataset of strings</h3>
<div id="outline-container-org682c748" class="outline-3">
<h3 id="org682c748"><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-orgac8b7d7" class="outline-3">
<h3 id="orgac8b7d7"><span class="section-number-3">1.7</span> Template for HDF5 has/read/write the string attribute</h3>
<div id="outline-container-org53326b9" class="outline-3">
<h3 id="org53326b9"><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: 2021-11-02 Tue 15:29</p>
<p class="date">Created: 2021-11-02 Tue 20:53</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>
<!-- 2021-11-02 Tue 15:29 -->
<!-- 2021-11-02 Tue 20:53 -->
<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="#org34a9a8e">1. TEXT back end</a>
<li><a href="#org2df7cd3">1. TEXT back end</a>
<ul>
<li><a href="#org2c0f79b">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#org9cfdeb8">1.2. Template for general structure in text back end</a></li>
<li><a href="#org800857b">1.3. Initialize function (constant part)</a></li>
<li><a href="#orgfbb55be">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#org2c2d0ba">1.5. Template for text read struct</a></li>
<li><a href="#orgc69cbaa">1.6. Template for text flush struct</a></li>
<li><a href="#org7d24b3f">1.7. Template for text free memory</a></li>
<li><a href="#orgd210803">1.8. Template for has/read/write the numerical attribute</a></li>
<li><a href="#orgf925db6">1.9. Template for has/read/write the dataset of numerical data</a></li>
<li><a href="#org642bc5e">1.10. Template for has/read/write the dataset of strings</a></li>
<li><a href="#orga360b8c">1.11. Template for has/read/write the string attribute</a></li>
<li><a href="#org385fd4e">1.12. RDM struct (hard-coded)</a>
<li><a href="#org3cecf01">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#org3faaf63">1.2. Template for general structure in text back end</a></li>
<li><a href="#orgb40fbd2">1.3. Initialize function (constant part)</a></li>
<li><a href="#org0aebae8">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#org01628dc">1.5. Template for text read struct</a></li>
<li><a href="#orgb264f33">1.6. Template for text flush struct</a></li>
<li><a href="#org7e27edd">1.7. Template for text free memory</a></li>
<li><a href="#org454df3f">1.8. Template for has/read/write the numerical attribute</a></li>
<li><a href="#org6fb1241">1.9. Template for has/read/write the dataset of numerical data</a></li>
<li><a href="#orgf07fdbf">1.10. Template for has/read/write the dataset of strings</a></li>
<li><a href="#org2544e32">1.11. Template for has/read/write the string attribute</a></li>
<li><a href="#orga40466e">1.12. RDM struct (hard-coded)</a>
<ul>
<li><a href="#org4c66f77">1.12.1. Read the complete struct</a></li>
<li><a href="#orgad2b8ee">1.12.2. Flush the complete struct</a></li>
<li><a href="#org3de14a1">1.12.3. Free memory</a></li>
<li><a href="#orgb415798">1.12.4. Read/Write the one<sub>e</sub> attribute</a></li>
<li><a href="#org4855773">1.12.5. Read/Write the two<sub>e</sub> attribute</a></li>
<li><a href="#org4a31597">1.12.1. Read the complete struct</a></li>
<li><a href="#org161420a">1.12.2. Flush the complete struct</a></li>
<li><a href="#org6e6675c">1.12.3. Free memory</a></li>
<li><a href="#org52d1d30">1.12.4. Read/Write the one<sub>e</sub> attribute</a></li>
<li><a href="#org4bffe1c">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-org34a9a8e" class="outline-2">
<h2 id="org34a9a8e"><span class="section-number-2">1</span> TEXT back end</h2>
<div id="outline-container-org2df7cd3" class="outline-2">
<h2 id="org2df7cd3"><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-org2c0f79b" class="outline-3">
<h3 id="org2c0f79b"><span class="section-number-3">1.1</span> Template for group-related structures in text back end</h3>
<div id="outline-container-org3cecf01" class="outline-3">
<h3 id="org3cecf01"><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-org9cfdeb8" class="outline-3">
<h3 id="org9cfdeb8"><span class="section-number-3">1.2</span> Template for general structure in text back end</h3>
<div id="outline-container-org3faaf63" class="outline-3">
<h3 id="org3faaf63"><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-org800857b" class="outline-3">
<h3 id="org800857b"><span class="section-number-3">1.3</span> Initialize function (constant part)</h3>
<div id="outline-container-orgb40fbd2" class="outline-3">
<h3 id="orgb40fbd2"><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-orgfbb55be" class="outline-3">
<h3 id="orgfbb55be"><span class="section-number-3">1.4</span> Deinitialize function (templated part)</h3>
<div id="outline-container-org0aebae8" class="outline-3">
<h3 id="org0aebae8"><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-org2c2d0ba" class="outline-3">
<h3 id="org2c2d0ba"><span class="section-number-3">1.5</span> Template for text read struct</h3>
<div id="outline-container-org01628dc" class="outline-3">
<h3 id="org01628dc"><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-orgc69cbaa" class="outline-3">
<h3 id="orgc69cbaa"><span class="section-number-3">1.6</span> Template for text flush struct</h3>
<div id="outline-container-orgb264f33" class="outline-3">
<h3 id="orgb264f33"><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-org7d24b3f" class="outline-3">
<h3 id="org7d24b3f"><span class="section-number-3">1.7</span> Template for text free memory</h3>
<div id="outline-container-org7e27edd" class="outline-3">
<h3 id="org7e27edd"><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-orgd210803" class="outline-3">
<h3 id="orgd210803"><span class="section-number-3">1.8</span> Template for has/read/write the numerical attribute</h3>
<div id="outline-container-org454df3f" class="outline-3">
<h3 id="org454df3f"><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-orgf925db6" class="outline-3">
<h3 id="orgf925db6"><span class="section-number-3">1.9</span> Template for has/read/write the dataset of numerical data</h3>
<div id="outline-container-org6fb1241" class="outline-3">
<h3 id="org6fb1241"><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-org642bc5e" class="outline-3">
<h3 id="org642bc5e"><span class="section-number-3">1.10</span> Template for has/read/write the dataset of strings</h3>
<div id="outline-container-orgf07fdbf" class="outline-3">
<h3 id="orgf07fdbf"><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-orga360b8c" class="outline-3">
<h3 id="orga360b8c"><span class="section-number-3">1.11</span> Template for has/read/write the string attribute</h3>
<div id="outline-container-org2544e32" class="outline-3">
<h3 id="org2544e32"><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-org385fd4e" class="outline-3">
<h3 id="org385fd4e"><span class="section-number-3">1.12</span> RDM struct (hard-coded)</h3>
<div id="outline-container-orga40466e" class="outline-3">
<h3 id="orga40466e"><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-org4c66f77" class="outline-4">
<h4 id="org4c66f77"><span class="section-number-4">1.12.1</span> Read the complete struct</h4>
<div id="outline-container-org4a31597" class="outline-4">
<h4 id="org4a31597"><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-orgad2b8ee" class="outline-4">
<h4 id="orgad2b8ee"><span class="section-number-4">1.12.2</span> Flush the complete struct</h4>
<div id="outline-container-org161420a" class="outline-4">
<h4 id="org161420a"><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-org3de14a1" class="outline-4">
<h4 id="org3de14a1"><span class="section-number-4">1.12.3</span> Free memory</h4>
<div id="outline-container-org6e6675c" class="outline-4">
<h4 id="org6e6675c"><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-orgb415798" class="outline-4">
<h4 id="orgb415798"><span class="section-number-4">1.12.4</span> Read/Write the one<sub>e</sub> attribute</h4>
<div id="outline-container-org52d1d30" class="outline-4">
<h4 id="org52d1d30"><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-org4855773" class="outline-4">
<h4 id="org4855773"><span class="section-number-4">1.12.5</span> Read/Write the two<sub>e</sub> attribute</h4>
<div id="outline-container-org4bffe1c" class="outline-4">
<h4 id="org4bffe1c"><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: 2021-11-02 Tue 15:29</p>
<p class="date">Created: 2021-11-02 Tue 20:53</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>
<!-- 2021-11-02 Tue 15:29 -->
<!-- 2021-11-02 Tue 20:53 -->
<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="#org9f4ef4a">1. Metadata (metadata group)</a></li>
<li><a href="#org597aa08">2. Electron (electron group)</a></li>
<li><a href="#org593bd08">3. Nucleus (nucleus group)</a></li>
<li><a href="#org1adb982">4. Effective core potentials (ecp group)</a>
<li><a href="#org7f592d3">1. Metadata (metadata group)</a></li>
<li><a href="#org2e622b1">2. Electron (electron group)</a></li>
<li><a href="#org6594a63">3. Nucleus (nucleus group)</a></li>
<li><a href="#orgf8690a1">4. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org9f32a2c">4.1. Example</a></li>
<li><a href="#orge15fc19">4.1. Example</a></li>
</ul>
</li>
<li><a href="#org0743870">5. Basis set (basis group)</a>
<li><a href="#org715a850">5. Basis set (basis group)</a>
<ul>
<li><a href="#orgb6e1a31">5.1. Example</a></li>
<li><a href="#orgc2a8e27">5.1. Example</a></li>
</ul>
</li>
<li><a href="#orgb1b0921">6. Atomic orbitals (ao group)</a>
<li><a href="#orgc5e869c">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="#org62c2a25">7. Molecular orbitals (mo group)</a>
<li><a href="#org059e4d9">7. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#orgca4d89a">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgac9d282">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org4c9e01d">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org93a9ea9">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#org62031e9">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#org4000e0d">9. <span class="todo TODO">TODO</span> Reduced density matrices (rdm group)</a></li>
<li><a href="#orgc1fe7d3">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#orgde21786">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-org9f4ef4a" class="outline-2">
<h2 id="org9f4ef4a"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org7f592d3" class="outline-2">
<h2 id="org7f592d3"><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="orga14419a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org56bfd3b" 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-org597aa08" class="outline-2">
<h2 id="org597aa08"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div id="outline-container-org2e622b1" class="outline-2">
<h2 id="org2e622b1"><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="org97592ef" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org6e68471" 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-org593bd08" class="outline-2">
<h2 id="org593bd08"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div id="outline-container-org6594a63" class="outline-2">
<h2 id="org6594a63"><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="org2d4006c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org78c1440" 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-org1adb982" class="outline-2">
<h2 id="org1adb982"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div id="outline-container-orgf8690a1" class="outline-2">
<h2 id="orgf8690a1"><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="orgb91937f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf724e31" 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-org9f32a2c" class="outline-3">
<h3 id="org9f32a2c"><span class="section-number-3">4.1</span> Example</h3>
<div id="outline-container-orge15fc19" class="outline-3">
<h3 id="orge15fc19"><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-org0743870" class="outline-2">
<h2 id="org0743870"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div id="outline-container-org715a850" class="outline-2">
<h2 id="org715a850"><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="org08dbe65" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org511019e" 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-orgb6e1a31" class="outline-3">
<h3 id="orgb6e1a31"><span class="section-number-3">5.1</span> Example</h3>
<div id="outline-container-orgc2a8e27" class="outline-3">
<h3 id="orgc2a8e27"><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-orgb1b0921" class="outline-2">
<h2 id="orgb1b0921"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div id="outline-container-orgc5e869c" class="outline-2">
<h2 id="orgc5e869c"><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="#org0743870">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#org715a850">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="org03776bb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd9c62c7" 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-orgb7d78b9" class="outline-3">
<h3 id="ao_one_e"><a id="orgb7d78b9"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div id="outline-container-org15f88a1" class="outline-3">
<h3 id="ao_one_e"><a id="org15f88a1"></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="org66f02ba" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org324ccdc" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1208,8 +1208,8 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org4cbb504" class="outline-3">
<h3 id="ao_two_e"><a id="org4cbb504"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div id="outline-container-orgb91bcd2" class="outline-3">
<h3 id="ao_two_e"><a id="orgb91bcd2"></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="org76e7e91" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org9dec8c0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1270,10 +1270,10 @@ notation.
</div>
</div>
<div id="outline-container-org62c2a25" class="outline-2">
<h2 id="org62c2a25"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div id="outline-container-org059e4d9" class="outline-2">
<h2 id="org059e4d9"><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="orgca4d89a"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
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<h3 id="org4c9e01d"><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="orgac9d282"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
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<h3 id="org93a9ea9"><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="org62031e9"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
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<h2 id="orgc1fe7d3"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
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<h2 id="org4000e0d"><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="orgde21786"><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: 2021-11-02 Tue 15:29</p>
<p class="date">Created: 2021-11-02 Tue 20:53</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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