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4
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>
<!-- 2021-11-19 Fri 11:51 -->
<!-- 2021-12-07 Tue 17:02 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name=google-site-verification content=jdDnuP2rYGJVy8AHSd-8LkmOmvK_dyz5buZ98wilYII />
@ -347,7 +347,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2021-11-19 Fri 11:51</p>
<p class="date">Created: 2021-12-07 Tue 17:02</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

16
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>
<!-- 2021-11-19 Fri 11:51 -->
<!-- 2021-12-07 Tue 17:02 -->
<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="#org5029027">1. Text back end</a></li>
<li><a href="#org3da0ee3">2. HDF5 Back end</a></li>
<li><a href="#org85d31a3">1. Text back end</a></li>
<li><a href="#org6e63f02">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-org5029027" class="outline-2">
<h2 id="org5029027"><span class="section-number-2">1</span> Text back end</h2>
<div id="outline-container-org85d31a3" class="outline-2">
<h2 id="org85d31a3"><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-org3da0ee3" class="outline-2">
<h2 id="org3da0ee3"><span class="section-number-2">2</span> HDF5 Back end</h2>
<div id="outline-container-org6e63f02" class="outline-2">
<h2 id="org6e63f02"><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: 2021-11-19 Fri 11:51</p>
<p class="date">Created: 2021-12-07 Tue 17:02</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>
<!-- 2021-11-19 Fri 11:51 -->
<!-- 2021-12-07 Tue 17:02 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name=google-site-verification content=jdDnuP2rYGJVy8AHSd-8LkmOmvK_dyz5buZ98wilYII />
@ -347,7 +347,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2021-11-19 Fri 11:51</p>
<p class="date">Created: 2021-12-07 Tue 17:02</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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@ -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>
<!-- 2021-11-19 Fri 11:51 -->
<!-- 2021-12-07 Tue 17:01 -->
<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="#orgba4eed0">1. Coding conventions</a>
<li><a href="#org8e97a9b">1. Coding conventions</a>
<ul>
<li><a href="#org460b57f">1.1. Memory allocation</a></li>
<li><a href="#orgb37e78a">1.1. Memory allocation</a></li>
</ul>
</li>
<li><a href="#org54ded64">2. Front end</a>
<li><a href="#org47ac5de">2. Front end</a>
<ul>
<li><a href="#org0f6164c">2.1. Error handling</a>
<li><a href="#org703493d">2.1. Error handling</a>
<ul>
<li><a href="#org868af34">2.1.1. Decoding errors</a>
<li><a href="#orgf22f73c">2.1.1. Decoding errors</a>
<ul>
<li><a href="#orgb97afe1">2.1.1.1. C source code</a></li>
<li><a href="#org25ea48e">2.1.1.2. Fortran interface</a></li>
<li><a href="#org5cae767">2.1.1.3. Python interface</a></li>
<li><a href="#org37762ed">2.1.1.1. C source code</a></li>
<li><a href="#orgc438221">2.1.1.2. Fortran interface</a></li>
<li><a href="#orgcd4ed77">2.1.1.3. Python interface</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org3bc77c2">2.2. Back ends</a>
<li><a href="#org10c01bc">2.2. Back ends</a>
<ul>
<li><a href="#org4813c44">2.2.1. C</a></li>
<li><a href="#orgd39293f">2.2.2. Fortran</a></li>
<li><a href="#org6ff09b0">2.2.3. Python</a></li>
<li><a href="#org13c082e">2.2.1. C</a></li>
<li><a href="#orgc77f7b3">2.2.2. Fortran</a></li>
<li><a href="#org406e461">2.2.3. Python</a></li>
</ul>
</li>
<li><a href="#org35efc31">2.3. Read/write behavior</a></li>
<li><a href="#orgbbf5fee">2.4. TREXIO file type</a>
<li><a href="#orgef02bff">2.3. Read/write behavior</a></li>
<li><a href="#org8a99fae">2.4. TREXIO file type</a>
<ul>
<li><a href="#org5fd6d24">2.4.1. TREXIO<sub>File</sub> Python class</a></li>
<li><a href="#orgf0aabc6">2.4.1. TREXIO<sub>File</sub> Python class</a></li>
</ul>
</li>
<li><a href="#org189eda1">2.5. Polymorphism of the file handle</a></li>
<li><a href="#org8f8d3e1">2.6. File opening</a>
<li><a href="#org1a0fb99">2.5. Polymorphism of the file handle</a></li>
<li><a href="#org380c573">2.6. File opening</a>
<ul>
<li><a href="#orgc429528">2.6.1. C</a></li>
<li><a href="#org7b117cb">2.6.2. Fortran</a></li>
<li><a href="#org51fbd6b">2.6.3. Python</a></li>
<li><a href="#orgc781d3f">2.6.4. Zero-based versus one-based arrays of indices</a></li>
<li><a href="#org7a272df">2.6.1. C</a></li>
<li><a href="#org2f00bc0">2.6.2. Fortran</a></li>
<li><a href="#orgc290910">2.6.3. Python</a></li>
<li><a href="#org40c4f7d">2.6.4. Zero-based versus one-based arrays of indices</a></li>
</ul>
</li>
<li><a href="#org02624e1">2.7. File closing</a>
<li><a href="#org0730bea">2.7. File closing</a>
<ul>
<li><a href="#org135d826">2.7.1. C</a></li>
<li><a href="#org3495270">2.7.2. Fortran</a></li>
<li><a href="#org9cd8358">2.7.3. Python</a></li>
<li><a href="#orgc87e084">2.7.1. C</a></li>
<li><a href="#org5973846">2.7.2. Fortran</a></li>
<li><a href="#org5ad78ff">2.7.3. Python</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org97aa1bc">3. Templates for front end</a>
<li><a href="#org5057e5d">3. Templates for front end</a>
<ul>
<li><a href="#org920802d">3.1. Description</a></li>
<li><a href="#orgbd7caa2">3.2. Templates for front end has/read/write a single numerical attribute</a>
<li><a href="#org8e73bc9">3.1. Description</a></li>
<li><a href="#org373c93b">3.2. Templates for front end has/read/write a single numerical attribute</a>
<ul>
<li><a href="#org776a2ca">3.2.1. Introduction</a></li>
<li><a href="#org3b919a2">3.2.2. C templates for front end</a>
<li><a href="#org4861253">3.2.1. Introduction</a></li>
<li><a href="#orgd634f99">3.2.2. C templates for front end</a>
<ul>
<li><a href="#org583623f">3.2.2.1. Function declarations</a></li>
<li><a href="#org0742994">3.2.2.2. Source code for double precision functions</a></li>
<li><a href="#orga916088">3.2.2.3. Source code for single precision functions</a></li>
<li><a href="#orgd45989c">3.2.2.4. Source code for default functions</a></li>
<li><a href="#orgdc5b9af">3.2.2.1. Function declarations</a></li>
<li><a href="#org00ec232">3.2.2.2. Source code for double precision functions</a></li>
<li><a href="#org0f829c4">3.2.2.3. Source code for single precision functions</a></li>
<li><a href="#orgfe56927">3.2.2.4. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#org2e4b69f">3.2.3. Fortran templates for front end</a></li>
<li><a href="#org11024e8">3.2.4. Python templates for front end</a></li>
<li><a href="#org43f897c">3.2.3. Fortran templates for front end</a></li>
<li><a href="#org6921c1a">3.2.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#orgcc5bba2">3.3. Templates for front end has/read/write a dataset of numerical data</a>
<li><a href="#org1daeba4">3.3. Templates for front end has/read/write a dataset of numerical data</a>
<ul>
<li><a href="#orgf8b64d6">3.3.1. Introduction</a></li>
<li><a href="#orga3c00e6">3.3.2. C templates for front end</a>
<li><a href="#org0f9e1f2">3.3.1. Introduction</a></li>
<li><a href="#org33bf2f2">3.3.2. C templates for front end</a>
<ul>
<li><a href="#org8792e8d">3.3.2.1. Function declarations</a></li>
<li><a href="#orgf1a6808">3.3.2.2. Source code for double precision functions</a></li>
<li><a href="#orgd97fdfc">3.3.2.3. Source code for single precision functions</a></li>
<li><a href="#org6f3fabb">3.3.2.4. Source code for memory-safe functions</a></li>
<li><a href="#orgce05abf">3.3.2.5. Source code for default functions</a></li>
<li><a href="#orgdbb5a8c">3.3.2.1. Function declarations</a></li>
<li><a href="#org52753b7">3.3.2.2. Source code for double precision functions</a></li>
<li><a href="#org85979a1">3.3.2.3. Source code for single precision functions</a></li>
<li><a href="#org1134d18">3.3.2.4. Source code for memory-safe functions</a></li>
<li><a href="#org1a3e2dd">3.3.2.5. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#orgd9bfc69">3.3.3. Fortran templates for front end</a></li>
<li><a href="#orgc53cb2c">3.3.4. Python templates for front end</a></li>
<li><a href="#org1619b97">3.3.3. Fortran templates for front end</a></li>
<li><a href="#org5de8f4f">3.3.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#org56981d1">3.4. Sparse data structures</a></li>
<li><a href="#org12e5949">3.5. Templates for front end has/read/write a dataset of strings</a>
<li><a href="#org4d13bf6">3.4. Sparse data structures</a></li>
<li><a href="#org9881784">3.5. Templates for front end has/read/write a dataset of strings</a>
<ul>
<li><a href="#org0ece56f">3.5.1. Introduction</a></li>
<li><a href="#orga1c13aa">3.5.2. C templates for front end</a>
<li><a href="#org8fc27d5">3.5.1. Introduction</a></li>
<li><a href="#orgf38cfd3">3.5.2. C templates for front end</a>
<ul>
<li><a href="#orgb483381">3.5.2.1. Function declarations</a></li>
<li><a href="#orgf4b4084">3.5.2.2. Source code for default functions</a></li>
<li><a href="#org309e967">3.5.2.1. Function declarations</a></li>
<li><a href="#org8f2758a">3.5.2.2. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#org4b94dee">3.5.3. Fortran templates for front end</a></li>
<li><a href="#org31bb600">3.5.4. Python templates for front end</a></li>
<li><a href="#org3725614">3.5.3. Fortran templates for front end</a></li>
<li><a href="#orgcee94db">3.5.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#org8c53555">3.6. Templates for front end has/read/write a single string attribute</a>
<li><a href="#org4a5036a">3.6. Templates for front end has/read/write a single string attribute</a>
<ul>
<li><a href="#orga98af5c">3.6.1. Introduction</a></li>
<li><a href="#orga476d0f">3.6.2. C templates for front end</a>
<li><a href="#org534958f">3.6.1. Introduction</a></li>
<li><a href="#org5541d8b">3.6.2. C templates for front end</a>
<ul>
<li><a href="#orgade2a6f">3.6.2.1. Function declarations</a></li>
<li><a href="#org70971d7">3.6.2.2. Source code for default functions</a></li>
<li><a href="#orgb9f07f7">3.6.2.1. Function declarations</a></li>
<li><a href="#org1b259df">3.6.2.2. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#org7749948">3.6.3. Fortran templates for front end</a></li>
<li><a href="#org5fd5999">3.6.4. Python templates for front end</a></li>
<li><a href="#org62d2c6b">3.6.3. Fortran templates for front end</a></li>
<li><a href="#org1a95988">3.6.4. Python templates for front end</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgb4f36e7">4. Fortran helper/wrapper functions</a></li>
<li><a href="#org6eea969">4. Fortran helper/wrapper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-orgba4eed0" class="outline-2">
<h2 id="orgba4eed0"><span class="section-number-2">1</span> Coding conventions</h2>
<div id="outline-container-org8e97a9b" class="outline-2">
<h2 id="org8e97a9b"><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-org460b57f" class="outline-3">
<h3 id="org460b57f"><span class="section-number-3">1.1</span> Memory allocation</h3>
<div id="outline-container-orgb37e78a" class="outline-3">
<h3 id="orgb37e78a"><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-org54ded64" class="outline-2">
<h2 id="org54ded64"><span class="section-number-2">2</span> Front end</h2>
<div id="outline-container-org47ac5de" class="outline-2">
<h2 id="org47ac5de"><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-org0f6164c" class="outline-3">
<h3 id="org0f6164c"><span class="section-number-3">2.1</span> Error handling</h3>
<div id="outline-container-org703493d" class="outline-3">
<h3 id="org703493d"><span class="section-number-3">2.1</span> Error handling</h3>
<div class="outline-text-3" id="text-2-1">
<table id="org3f9f3f2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org4d746fa" 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-org868af34" class="outline-4">
<h4 id="org868af34"><span class="section-number-4">2.1.1</span> Decoding errors</h4>
<div id="outline-container-orgf22f73c" class="outline-4">
<h4 id="orgf22f73c"><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-orgb97afe1" class="outline-5">
<h5 id="orgb97afe1"><span class="section-number-5">2.1.1.1</span> C source code</h5>
<div id="outline-container-org37762ed" class="outline-5">
<h5 id="org37762ed"><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-org25ea48e" class="outline-5">
<h5 id="org25ea48e"><span class="section-number-5">2.1.1.2</span> Fortran interface</h5>
<div id="outline-container-orgc438221" class="outline-5">
<h5 id="orgc438221"><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-org5cae767" class="outline-5">
<h5 id="org5cae767"><span class="section-number-5">2.1.1.3</span> Python interface</h5>
<div id="outline-container-orgcd4ed77" class="outline-5">
<h5 id="orgcd4ed77"><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-org3bc77c2" class="outline-3">
<h3 id="org3bc77c2"><span class="section-number-3">2.2</span> Back ends</h3>
<div id="outline-container-org10c01bc" class="outline-3">
<h3 id="org10c01bc"><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-org4813c44" class="outline-4">
<h4 id="org4813c44"><span class="section-number-4">2.2.1</span> C</h4>
<div id="outline-container-org13c082e" class="outline-4">
<h4 id="org13c082e"><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-orgd39293f" class="outline-4">
<h4 id="orgd39293f"><span class="section-number-4">2.2.2</span> Fortran</h4>
<div id="outline-container-orgc77f7b3" class="outline-4">
<h4 id="orgc77f7b3"><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-org6ff09b0" class="outline-4">
<h4 id="org6ff09b0"><span class="section-number-4">2.2.3</span> Python</h4>
<div id="outline-container-org406e461" class="outline-4">
<h4 id="org406e461"><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-org35efc31" class="outline-3">
<h3 id="org35efc31"><span class="section-number-3">2.3</span> Read/write behavior</h3>
<div id="outline-container-orgef02bff" class="outline-3">
<h3 id="orgef02bff"><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-orgbbf5fee" class="outline-3">
<h3 id="orgbbf5fee"><span class="section-number-3">2.4</span> TREXIO file type</h3>
<div id="outline-container-org8a99fae" class="outline-3">
<h3 id="org8a99fae"><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-org5fd6d24" class="outline-4">
<h4 id="org5fd6d24"><span class="section-number-4">2.4.1</span> TREXIO<sub>File</sub> Python class</h4>
<div id="outline-container-orgf0aabc6" class="outline-4">
<h4 id="orgf0aabc6"><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-org189eda1" class="outline-3">
<h3 id="org189eda1"><span class="section-number-3">2.5</span> Polymorphism of the file handle</h3>
<div id="outline-container-org1a0fb99" class="outline-3">
<h3 id="org1a0fb99"><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-org8f8d3e1" class="outline-3">
<h3 id="org8f8d3e1"><span class="section-number-3">2.6</span> File opening</h3>
<div id="outline-container-org380c573" class="outline-3">
<h3 id="org380c573"><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-orgc429528" class="outline-4">
<h4 id="orgc429528"><span class="section-number-4">2.6.1</span> C</h4>
<div id="outline-container-org7a272df" class="outline-4">
<h4 id="org7a272df"><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-org7b117cb" class="outline-4">
<h4 id="org7b117cb"><span class="section-number-4">2.6.2</span> Fortran</h4>
<div id="outline-container-org2f00bc0" class="outline-4">
<h4 id="org2f00bc0"><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-org51fbd6b" class="outline-4">
<h4 id="org51fbd6b"><span class="section-number-4">2.6.3</span> Python</h4>
<div id="outline-container-orgc290910" class="outline-4">
<h4 id="orgc290910"><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-orgc781d3f" class="outline-4">
<h4 id="orgc781d3f"><span class="section-number-4">2.6.4</span> Zero-based versus one-based arrays of indices</h4>
<div id="outline-container-org40c4f7d" class="outline-4">
<h4 id="org40c4f7d"><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-org02624e1" class="outline-3">
<h3 id="org02624e1"><span class="section-number-3">2.7</span> File closing</h3>
<div id="outline-container-org0730bea" class="outline-3">
<h3 id="org0730bea"><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-org135d826" class="outline-4">
<h4 id="org135d826"><span class="section-number-4">2.7.1</span> C</h4>
<div id="outline-container-orgc87e084" class="outline-4">
<h4 id="orgc87e084"><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-org3495270" class="outline-4">
<h4 id="org3495270"><span class="section-number-4">2.7.2</span> Fortran</h4>
<div id="outline-container-org5973846" class="outline-4">
<h4 id="org5973846"><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-org9cd8358" class="outline-4">
<h4 id="org9cd8358"><span class="section-number-4">2.7.3</span> Python</h4>
<div id="outline-container-org5ad78ff" class="outline-4">
<h4 id="org5ad78ff"><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-org97aa1bc" class="outline-2">
<h2 id="org97aa1bc"><span class="section-number-2">3</span> Templates for front end</h2>
<div id="outline-container-org5057e5d" class="outline-2">
<h2 id="org5057e5d"><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-org920802d" class="outline-3">
<h3 id="org920802d"><span class="section-number-3">3.1</span> Description</h3>
<div id="outline-container-org8e73bc9" class="outline-3">
<h3 id="org8e73bc9"><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-orgbd7caa2" class="outline-3">
<h3 id="orgbd7caa2"><span class="section-number-3">3.2</span> Templates for front end has/read/write a single numerical attribute</h3>
<div id="outline-container-org373c93b" class="outline-3">
<h3 id="org373c93b"><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-org776a2ca" class="outline-4">
<h4 id="org776a2ca"><span class="section-number-4">3.2.1</span> Introduction</h4>
<div id="outline-container-org4861253" class="outline-4">
<h4 id="org4861253"><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-org3b919a2" class="outline-4">
<h4 id="org3b919a2"><span class="section-number-4">3.2.2</span> C templates for front end</h4>
<div id="outline-container-orgd634f99" class="outline-4">
<h4 id="orgd634f99"><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-org583623f" class="outline-5">
<h5 id="org583623f"><span class="section-number-5">3.2.2.1</span> Function declarations</h5>
<div id="outline-container-orgdc5b9af" class="outline-5">
<h5 id="orgdc5b9af"><span class="section-number-5">3.2.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-org0742994" class="outline-5">
<h5 id="org0742994"><span class="section-number-5">3.2.2.2</span> Source code for double precision functions</h5>
<div id="outline-container-org00ec232" class="outline-5">
<h5 id="org00ec232"><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-orga916088" class="outline-5">
<h5 id="orga916088"><span class="section-number-5">3.2.2.3</span> Source code for single precision functions</h5>
<div id="outline-container-org0f829c4" class="outline-5">
<h5 id="org0f829c4"><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-orgd45989c" class="outline-5">
<h5 id="orgd45989c"><span class="section-number-5">3.2.2.4</span> Source code for default functions</h5>
<div id="outline-container-orgfe56927" class="outline-5">
<h5 id="orgfe56927"><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-org2e4b69f" class="outline-4">
<h4 id="org2e4b69f"><span class="section-number-4">3.2.3</span> Fortran templates for front end</h4>
<div id="outline-container-org43f897c" class="outline-4">
<h4 id="org43f897c"><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-org11024e8" class="outline-4">
<h4 id="org11024e8"><span class="section-number-4">3.2.4</span> Python templates for front end</h4>
<div id="outline-container-org6921c1a" class="outline-4">
<h4 id="org6921c1a"><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-orgcc5bba2" class="outline-3">
<h3 id="orgcc5bba2"><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-org1daeba4" class="outline-3">
<h3 id="org1daeba4"><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-orgf8b64d6" class="outline-4">
<h4 id="orgf8b64d6"><span class="section-number-4">3.3.1</span> Introduction</h4>
<div id="outline-container-org0f9e1f2" class="outline-4">
<h4 id="org0f9e1f2"><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-orga3c00e6" class="outline-4">
<h4 id="orga3c00e6"><span class="section-number-4">3.3.2</span> C templates for front end</h4>
<div id="outline-container-org33bf2f2" class="outline-4">
<h4 id="org33bf2f2"><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-org8792e8d" class="outline-5">
<h5 id="org8792e8d"><span class="section-number-5">3.3.2.1</span> Function declarations</h5>
<div id="outline-container-orgdbb5a8c" class="outline-5">
<h5 id="orgdbb5a8c"><span class="section-number-5">3.3.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-orgf1a6808" class="outline-5">
<h5 id="orgf1a6808"><span class="section-number-5">3.3.2.2</span> Source code for double precision functions</h5>
<div id="outline-container-org52753b7" class="outline-5">
<h5 id="org52753b7"><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-orgd97fdfc" class="outline-5">
<h5 id="orgd97fdfc"><span class="section-number-5">3.3.2.3</span> Source code for single precision functions</h5>
<div id="outline-container-org85979a1" class="outline-5">
<h5 id="org85979a1"><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-org6f3fabb" class="outline-5">
<h5 id="org6f3fabb"><span class="section-number-5">3.3.2.4</span> Source code for memory-safe functions</h5>
<div id="outline-container-org1134d18" class="outline-5">
<h5 id="org1134d18"><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="orgb9dfdc0"><span style="color: #228b22;">trexio_exit_code</span> <span style="color: #a0522d;">rc</span>;
<pre class="src src-c" id="org911a490"><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-orgce05abf" class="outline-5">
<h5 id="orgce05abf"><span class="section-number-5">3.3.2.5</span> Source code for default functions</h5>
<div id="outline-container-org1a3e2dd" class="outline-5">
<h5 id="org1a3e2dd"><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-orgd9bfc69" class="outline-4">
<h4 id="orgd9bfc69"><span class="section-number-4">3.3.3</span> Fortran templates for front end</h4>
<div id="outline-container-org1619b97" class="outline-4">
<h4 id="org1619b97"><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-orgc53cb2c" class="outline-4">
<h4 id="orgc53cb2c"><span class="section-number-4">3.3.4</span> Python templates for front end</h4>
<div id="outline-container-org5de8f4f" class="outline-4">
<h4 id="org5de8f4f"><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-org56981d1" class="outline-3">
<h3 id="org56981d1"><span class="section-number-3">3.4</span> Sparse data structures</h3>
<div id="outline-container-org4d13bf6" class="outline-3">
<h3 id="org4d13bf6"><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-org12e5949" class="outline-3">
<h3 id="org12e5949"><span class="section-number-3">3.5</span> Templates for front end has/read/write a dataset of strings</h3>
<div id="outline-container-org9881784" class="outline-3">
<h3 id="org9881784"><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-org0ece56f" class="outline-4">
<h4 id="org0ece56f"><span class="section-number-4">3.5.1</span> Introduction</h4>
<div id="outline-container-org8fc27d5" class="outline-4">
<h4 id="org8fc27d5"><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-orga1c13aa" class="outline-4">
<h4 id="orga1c13aa"><span class="section-number-4">3.5.2</span> C templates for front end</h4>
<div id="outline-container-orgf38cfd3" class="outline-4">
<h4 id="orgf38cfd3"><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-orgb483381" class="outline-5">
<h5 id="orgb483381"><span class="section-number-5">3.5.2.1</span> Function declarations</h5>
<div id="outline-container-org309e967" class="outline-5">
<h5 id="org309e967"><span class="section-number-5">3.5.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-orgf4b4084" class="outline-5">
<h5 id="orgf4b4084"><span class="section-number-5">3.5.2.2</span> Source code for default functions</h5>
<div id="outline-container-org8f2758a" class="outline-5">
<h5 id="org8f2758a"><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-org4b94dee" class="outline-4">
<h4 id="org4b94dee"><span class="section-number-4">3.5.3</span> Fortran templates for front end</h4>
<div id="outline-container-org3725614" class="outline-4">
<h4 id="org3725614"><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-org31bb600" class="outline-4">
<h4 id="org31bb600"><span class="section-number-4">3.5.4</span> Python templates for front end</h4>
<div id="outline-container-orgcee94db" class="outline-4">
<h4 id="orgcee94db"><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-org8c53555" class="outline-3">
<h3 id="org8c53555"><span class="section-number-3">3.6</span> Templates for front end has/read/write a single string attribute</h3>
<div id="outline-container-org4a5036a" class="outline-3">
<h3 id="org4a5036a"><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-orga98af5c" class="outline-4">
<h4 id="orga98af5c"><span class="section-number-4">3.6.1</span> Introduction</h4>
<div id="outline-container-org534958f" class="outline-4">
<h4 id="org534958f"><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-orga476d0f" class="outline-4">
<h4 id="orga476d0f"><span class="section-number-4">3.6.2</span> C templates for front end</h4>
<div id="outline-container-org5541d8b" class="outline-4">
<h4 id="org5541d8b"><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-orgade2a6f" class="outline-5">
<h5 id="orgade2a6f"><span class="section-number-5">3.6.2.1</span> Function declarations</h5>
<div id="outline-container-orgb9f07f7" class="outline-5">
<h5 id="orgb9f07f7"><span class="section-number-5">3.6.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-org70971d7" class="outline-5">
<h5 id="org70971d7"><span class="section-number-5">3.6.2.2</span> Source code for default functions</h5>
<div id="outline-container-org1b259df" class="outline-5">
<h5 id="org1b259df"><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-org7749948" class="outline-4">
<h4 id="org7749948"><span class="section-number-4">3.6.3</span> Fortran templates for front end</h4>
<div id="outline-container-org62d2c6b" class="outline-4">
<h4 id="org62d2c6b"><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-org5fd5999" class="outline-4">
<h4 id="org5fd5999"><span class="section-number-4">3.6.4</span> Python templates for front end</h4>
<div id="outline-container-org1a95988" class="outline-4">
<h4 id="org1a95988"><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-orgb4f36e7" class="outline-2">
<h2 id="orgb4f36e7"><span class="section-number-2">4</span> Fortran helper/wrapper functions</h2>
<div id="outline-container-org6eea969" class="outline-2">
<h2 id="org6eea969"><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: 2021-11-19 Fri 11:51</p>
<p class="date">Created: 2021-12-07 Tue 17:01</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>
<!-- 2021-11-19 Fri 11:51 -->
<!-- 2021-12-07 Tue 17:02 -->
<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="#orgbc0b849">1. HDF5 back end</a>
<li><a href="#org3d178cb">1. HDF5 back end</a>
<ul>
<li><a href="#orge9613be">1.1. Template for HDF5 definitions</a></li>
<li><a href="#org773a085">1.2. Template for HDF5 structures</a></li>
<li><a href="#org0387c9b">1.3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgcacb526">1.4. Template for HDF5 has/read/write the numerical attribute</a></li>
<li><a href="#org67645d8">1.5. Template for HDF5 has/read/write the dataset of numerical data</a></li>
<li><a href="#org8e9c0d9">1.6. Template for HDF5 has/read/write the dataset of strings</a></li>
<li><a href="#orge0989d3">1.7. Template for HDF5 has/read/write the string attribute</a></li>
<li><a href="#orgea8f208">1.1. Template for HDF5 definitions</a></li>
<li><a href="#org2114022">1.2. Template for HDF5 structures</a></li>
<li><a href="#org86fbe24">1.3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgffaa4b9">1.4. Template for HDF5 has/read/write the numerical attribute</a></li>
<li><a href="#org70a8c0d">1.5. Template for HDF5 has/read/write the dataset of numerical data</a></li>
<li><a href="#org3bc110b">1.6. Template for HDF5 has/read/write the dataset of strings</a></li>
<li><a href="#org3f41223">1.7. Template for HDF5 has/read/write the string attribute</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-orgbc0b849" class="outline-2">
<h2 id="orgbc0b849"><span class="section-number-2">1</span> HDF5 back end</h2>
<div id="outline-container-org3d178cb" class="outline-2">
<h2 id="org3d178cb"><span class="section-number-2">1</span> HDF5 back end</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-orge9613be" class="outline-3">
<h3 id="orge9613be"><span class="section-number-3">1.1</span> Template for HDF5 definitions</h3>
<div id="outline-container-orgea8f208" class="outline-3">
<h3 id="orgea8f208"><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-org773a085" class="outline-3">
<h3 id="org773a085"><span class="section-number-3">1.2</span> Template for HDF5 structures</h3>
<div id="outline-container-org2114022" class="outline-3">
<h3 id="org2114022"><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-org0387c9b" class="outline-3">
<h3 id="org0387c9b"><span class="section-number-3">1.3</span> Template for HDF5 init/deinit</h3>
<div id="outline-container-org86fbe24" class="outline-3">
<h3 id="org86fbe24"><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-orgcacb526" class="outline-3">
<h3 id="orgcacb526"><span class="section-number-3">1.4</span> Template for HDF5 has/read/write the numerical attribute</h3>
<div id="outline-container-orgffaa4b9" class="outline-3">
<h3 id="orgffaa4b9"><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-org67645d8" class="outline-3">
<h3 id="org67645d8"><span class="section-number-3">1.5</span> Template for HDF5 has/read/write the dataset of numerical data</h3>
<div id="outline-container-org70a8c0d" class="outline-3">
<h3 id="org70a8c0d"><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-org8e9c0d9" class="outline-3">
<h3 id="org8e9c0d9"><span class="section-number-3">1.6</span> Template for HDF5 has/read/write the dataset of strings</h3>
<div id="outline-container-org3bc110b" class="outline-3">
<h3 id="org3bc110b"><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-orge0989d3" class="outline-3">
<h3 id="orge0989d3"><span class="section-number-3">1.7</span> Template for HDF5 has/read/write the string attribute</h3>
<div id="outline-container-org3f41223" class="outline-3">
<h3 id="org3f41223"><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: 2021-11-19 Fri 11:51</p>
<p class="date">Created: 2021-12-07 Tue 17:02</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>
<!-- 2021-11-19 Fri 11:51 -->
<!-- 2021-12-07 Tue 17:02 -->
<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="#orgc178bed">1. TEXT back end</a>
<li><a href="#org8879338">1. TEXT back end</a>
<ul>
<li><a href="#org45aa88e">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#org274fb8d">1.2. Template for general structure in text back end</a></li>
<li><a href="#org1fbf9eb">1.3. Initialize function (constant part)</a></li>
<li><a href="#org01656b0">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#org0f67fb9">1.5. Template for text read struct</a></li>
<li><a href="#org1ed6ff7">1.6. Template for text flush struct</a></li>
<li><a href="#orgac72974">1.7. Template for text free memory</a></li>
<li><a href="#org7fc9d12">1.8. Template for has/read/write the numerical attribute</a></li>
<li><a href="#org894bc22">1.9. Template for has/read/write the dataset of numerical data</a></li>
<li><a href="#org3bc497d">1.10. Template for has/read/write the dataset of strings</a></li>
<li><a href="#org8c9e2e2">1.11. Template for has/read/write the string attribute</a></li>
<li><a href="#org7b99a5a">1.12. RDM struct (hard-coded)</a>
<li><a href="#orgb150be4">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#org97f70d9">1.2. Template for general structure in text back end</a></li>
<li><a href="#org0f87b54">1.3. Initialize function (constant part)</a></li>
<li><a href="#orgbf4fd31">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#orgc9acbf0">1.5. Template for text read struct</a></li>
<li><a href="#orgfcb7eb6">1.6. Template for text flush struct</a></li>
<li><a href="#org9a42075">1.7. Template for text free memory</a></li>
<li><a href="#org35bb2cc">1.8. Template for has/read/write the numerical attribute</a></li>
<li><a href="#org6e5b901">1.9. Template for has/read/write the dataset of numerical data</a></li>
<li><a href="#org5e4cf88">1.10. Template for has/read/write the dataset of strings</a></li>
<li><a href="#org3d1036a">1.11. Template for has/read/write the string attribute</a></li>
<li><a href="#orgc234938">1.12. RDM struct (hard-coded)</a>
<ul>
<li><a href="#org781df1c">1.12.1. Read the complete struct</a></li>
<li><a href="#orgf1e91a4">1.12.2. Flush the complete struct</a></li>
<li><a href="#org578754e">1.12.3. Free memory</a></li>
<li><a href="#org5fef976">1.12.4. Read/Write the one<sub>e</sub> attribute</a></li>
<li><a href="#orgbafbb5b">1.12.5. Read/Write the two<sub>e</sub> attribute</a></li>
<li><a href="#orgec3be76">1.12.1. Read the complete struct</a></li>
<li><a href="#org86d4cac">1.12.2. Flush the complete struct</a></li>
<li><a href="#org2c41d1d">1.12.3. Free memory</a></li>
<li><a href="#org51590f7">1.12.4. Read/Write the one<sub>e</sub> attribute</a></li>
<li><a href="#org3627914">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-orgc178bed" class="outline-2">
<h2 id="orgc178bed"><span class="section-number-2">1</span> TEXT back end</h2>
<div id="outline-container-org8879338" class="outline-2">
<h2 id="org8879338"><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-org45aa88e" class="outline-3">
<h3 id="org45aa88e"><span class="section-number-3">1.1</span> Template for group-related structures in text back end</h3>
<div id="outline-container-orgb150be4" class="outline-3">
<h3 id="orgb150be4"><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-org274fb8d" class="outline-3">
<h3 id="org274fb8d"><span class="section-number-3">1.2</span> Template for general structure in text back end</h3>
<div id="outline-container-org97f70d9" class="outline-3">
<h3 id="org97f70d9"><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-org1fbf9eb" class="outline-3">
<h3 id="org1fbf9eb"><span class="section-number-3">1.3</span> Initialize function (constant part)</h3>
<div id="outline-container-org0f87b54" class="outline-3">
<h3 id="org0f87b54"><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-org01656b0" class="outline-3">
<h3 id="org01656b0"><span class="section-number-3">1.4</span> Deinitialize function (templated part)</h3>
<div id="outline-container-orgbf4fd31" class="outline-3">
<h3 id="orgbf4fd31"><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-org0f67fb9" class="outline-3">
<h3 id="org0f67fb9"><span class="section-number-3">1.5</span> Template for text read struct</h3>
<div id="outline-container-orgc9acbf0" class="outline-3">
<h3 id="orgc9acbf0"><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-org1ed6ff7" class="outline-3">
<h3 id="org1ed6ff7"><span class="section-number-3">1.6</span> Template for text flush struct</h3>
<div id="outline-container-orgfcb7eb6" class="outline-3">
<h3 id="orgfcb7eb6"><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-orgac72974" class="outline-3">
<h3 id="orgac72974"><span class="section-number-3">1.7</span> Template for text free memory</h3>
<div id="outline-container-org9a42075" class="outline-3">
<h3 id="org9a42075"><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-org7fc9d12" class="outline-3">
<h3 id="org7fc9d12"><span class="section-number-3">1.8</span> Template for has/read/write the numerical attribute</h3>
<div id="outline-container-org35bb2cc" class="outline-3">
<h3 id="org35bb2cc"><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-org894bc22" class="outline-3">
<h3 id="org894bc22"><span class="section-number-3">1.9</span> Template for has/read/write the dataset of numerical data</h3>
<div id="outline-container-org6e5b901" class="outline-3">
<h3 id="org6e5b901"><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-org3bc497d" class="outline-3">
<h3 id="org3bc497d"><span class="section-number-3">1.10</span> Template for has/read/write the dataset of strings</h3>
<div id="outline-container-org5e4cf88" class="outline-3">
<h3 id="org5e4cf88"><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-org8c9e2e2" class="outline-3">
<h3 id="org8c9e2e2"><span class="section-number-3">1.11</span> Template for has/read/write the string attribute</h3>
<div id="outline-container-org3d1036a" class="outline-3">
<h3 id="org3d1036a"><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-org7b99a5a" class="outline-3">
<h3 id="org7b99a5a"><span class="section-number-3">1.12</span> RDM struct (hard-coded)</h3>
<div id="outline-container-orgc234938" class="outline-3">
<h3 id="orgc234938"><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-org781df1c" class="outline-4">
<h4 id="org781df1c"><span class="section-number-4">1.12.1</span> Read the complete struct</h4>
<div id="outline-container-orgec3be76" class="outline-4">
<h4 id="orgec3be76"><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-orgf1e91a4" class="outline-4">
<h4 id="orgf1e91a4"><span class="section-number-4">1.12.2</span> Flush the complete struct</h4>
<div id="outline-container-org86d4cac" class="outline-4">
<h4 id="org86d4cac"><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-org578754e" class="outline-4">
<h4 id="org578754e"><span class="section-number-4">1.12.3</span> Free memory</h4>
<div id="outline-container-org2c41d1d" class="outline-4">
<h4 id="org2c41d1d"><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-org5fef976" class="outline-4">
<h4 id="org5fef976"><span class="section-number-4">1.12.4</span> Read/Write the one<sub>e</sub> attribute</h4>
<div id="outline-container-org51590f7" class="outline-4">
<h4 id="org51590f7"><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-orgbafbb5b" class="outline-4">
<h4 id="orgbafbb5b"><span class="section-number-4">1.12.5</span> Read/Write the two<sub>e</sub> attribute</h4>
<div id="outline-container-org3627914" class="outline-4">
<h4 id="org3627914"><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: 2021-11-19 Fri 11:51</p>
<p class="date">Created: 2021-12-07 Tue 17:02</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

120
trex.html
View File

@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2021-11-19 Fri 11:51 -->
<!-- 2021-12-07 Tue 17:02 -->
<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="#org41b9d88">1. Metadata (metadata group)</a></li>
<li><a href="#orgcc3c94e">2. Electron (electron group)</a></li>
<li><a href="#orgf0320fc">3. Nucleus (nucleus group)</a></li>
<li><a href="#orgd56c060">4. Effective core potentials (ecp group)</a>
<li><a href="#org2c77b4a">1. Metadata (metadata group)</a></li>
<li><a href="#orged59845">2. Electron (electron group)</a></li>
<li><a href="#org0ecd57e">3. Nucleus (nucleus group)</a></li>
<li><a href="#org4eb200c">4. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#orgc92ea81">4.1. Example</a></li>
<li><a href="#org3b400be">4.1. Example</a></li>
</ul>
</li>
<li><a href="#orge91f015">5. Basis set (basis group)</a>
<li><a href="#org732ed3b">5. Basis set (basis group)</a>
<ul>
<li><a href="#org43f6490">5.1. Example</a></li>
<li><a href="#org4f6a51b">5.1. Example</a></li>
</ul>
</li>
<li><a href="#org000bf19">6. Atomic orbitals (ao group)</a>
<li><a href="#org030c6ff">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="#org3bfd98d">7. Molecular orbitals (mo group)</a>
<li><a href="#org6d28a9e">7. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#orge0f3090">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org8bcef41">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org600602e">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org37f34bf">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#orgff3237f">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#org9aaa0ff">9. <span class="todo TODO">TODO</span> Reduced density matrices (rdm group)</a></li>
<li><a href="#org66e3b79">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#orgdca46a8">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-org41b9d88" class="outline-2">
<h2 id="org41b9d88"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org2c77b4a" class="outline-2">
<h2 id="org2c77b4a"><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="org7c61462" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org8fde4c1" 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-orgcc3c94e" class="outline-2">
<h2 id="orgcc3c94e"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div id="outline-container-orged59845" class="outline-2">
<h2 id="orged59845"><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="orge3a8b40" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org23c696f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -508,14 +508,14 @@ the number of &uarr; and &darr; electrons is fixed.
<tbody>
<tr>
<td class="org-left"><code>up_num</code></td>
<td class="org-left"><code>dim</code></td>
<td class="org-left"><code>int</code></td>
<td class="org-left">&#xa0;</td>
<td class="org-left">Number of &uarr;-spin electrons</td>
</tr>
<tr>
<td class="org-left"><code>dn_num</code></td>
<td class="org-left"><code>dim</code></td>
<td class="org-left"><code>int</code></td>
<td class="org-left">&#xa0;</td>
<td class="org-left">Number of &darr;-spin electrons</td>
</tr>
@ -524,15 +524,15 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-orgf0320fc" class="outline-2">
<h2 id="orgf0320fc"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div id="outline-container-org0ecd57e" class="outline-2">
<h2 id="org0ecd57e"><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="orga68aa40" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga69e626" 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-orgd56c060" class="outline-2">
<h2 id="orgd56c060"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div id="outline-container-org4eb200c" class="outline-2">
<h2 id="org4eb200c"><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="orgcb8d2f1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org7b2b137" 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-orgc92ea81" class="outline-3">
<h3 id="orgc92ea81"><span class="section-number-3">4.1</span> Example</h3>
<div id="outline-container-org3b400be" class="outline-3">
<h3 id="org3b400be"><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-orge91f015" class="outline-2">
<h2 id="orge91f015"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div id="outline-container-org732ed3b" class="outline-2">
<h2 id="org732ed3b"><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="orgde6c0e5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org6e40673" 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-org43f6490" class="outline-3">
<h3 id="org43f6490"><span class="section-number-3">5.1</span> Example</h3>
<div id="outline-container-org4f6a51b" class="outline-3">
<h3 id="org4f6a51b"><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-org000bf19" class="outline-2">
<h2 id="org000bf19"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div id="outline-container-org030c6ff" class="outline-2">
<h2 id="org030c6ff"><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="#orge91f015">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#org732ed3b">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="org407bdfe" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge8780d8" 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-org5a8abcc" class="outline-3">
<h3 id="ao_one_e"><a id="org5a8abcc"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div id="outline-container-org1f7b2e0" class="outline-3">
<h3 id="ao_one_e"><a id="org1f7b2e0"></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="org3dbe0e0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org7e00678" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1208,8 +1208,8 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-orgf50d1ad" class="outline-3">
<h3 id="ao_two_e"><a id="orgf50d1ad"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div id="outline-container-orgfcaeddc" class="outline-3">
<h3 id="ao_two_e"><a id="orgfcaeddc"></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>
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<colgroup>
@ -1270,10 +1270,10 @@ notation.
</div>
</div>
<div id="outline-container-org3bfd98d" class="outline-2">
<h2 id="org3bfd98d"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div id="outline-container-org6d28a9e" class="outline-2">
<h2 id="org6d28a9e"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div class="outline-text-2" id="text-7">
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<colgroup>
@ -1339,8 +1339,8 @@ notation.
</table>
</div>
<div id="outline-container-orge0f3090" class="outline-3">
<h3 id="orge0f3090"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div id="outline-container-org600602e" class="outline-3">
<h3 id="org600602e"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div class="outline-text-3" id="text-7-1">
<p>
The operators as the same as those defined in the
@ -1348,7 +1348,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
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<colgroup>
@ -1415,8 +1415,8 @@ the basis of molecular orbitals.
</div>
</div>
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<h3 id="org8bcef41"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div id="outline-container-org37f34bf" class="outline-3">
<h3 id="org37f34bf"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div class="outline-text-3" id="text-7-2">
<p>
The operators as the same as those defined in the
@ -1424,7 +1424,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
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<colgroup>
@ -1464,13 +1464,13 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-orgff3237f" class="outline-2">
<h2 id="orgff3237f"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
<div id="outline-container-org66e3b79" class="outline-2">
<h2 id="org66e3b79"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
</div>
<div id="outline-container-org9aaa0ff" class="outline-2">
<h2 id="org9aaa0ff"><span class="section-number-2">9</span> <span class="todo TODO">TODO</span> Reduced density matrices (rdm group)</h2>
<div id="outline-container-orgdca46a8" class="outline-2">
<h2 id="orgdca46a8"><span class="section-number-2">9</span> <span class="todo TODO">TODO</span> Reduced density matrices (rdm group)</h2>
<div class="outline-text-2" id="text-9">
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<colgroup>
@ -1525,7 +1525,7 @@ the basis of molecular orbitals.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2021-11-19 Fri 11:51</p>
<p class="date">Created: 2021-12-07 Tue 17:02</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>