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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>
<!-- 2021-09-24 Fri 10:46 -->
<!-- 2021-09-30 Thu 19:47 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title>
@ -349,7 +349,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2021-09-24 Fri 10:46</p>
<p class="date">Created: 2021-09-30 Thu 19:47</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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Sparse.html
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2021-09-24 Fri 10:46 -->
<!-- 2021-09-30 Thu 19:47 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>&lrm;</title>
@ -232,8 +232,8 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orge1cb130">1. Text back end</a></li>
<li><a href="#org4b614b1">2. HDF5 Back end</a></li>
<li><a href="#org4a9f0ff">1. Text back end</a></li>
<li><a href="#orge9fa5ff">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-orge1cb130" class="outline-2">
<h2 id="orge1cb130"><span class="section-number-2">1</span> Text back end</h2>
<div id="outline-container-org4a9f0ff" class="outline-2">
<h2 id="org4a9f0ff"><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-org4b614b1" class="outline-2">
<h2 id="org4b614b1"><span class="section-number-2">2</span> HDF5 Back end</h2>
<div id="outline-container-orge9fa5ff" class="outline-2">
<h2 id="orge9fa5ff"><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: 2021-09-24 Fri 10:46</p>
<p class="date">Created: 2021-09-30 Thu 19:47</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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index.html
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2021-09-24 Fri 10:46 -->
<!-- 2021-09-30 Thu 19:47 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title>
@ -349,7 +349,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2021-09-24 Fri 10:46</p>
<p class="date">Created: 2021-09-30 Thu 19:47</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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templator_front.html
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@ -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>
<!-- 2021-09-24 Fri 10:46 -->
<!-- 2021-09-30 Thu 19:47 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Front end API</title>
@ -339,125 +339,125 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org1e9450f">1. Coding conventions</a>
<li><a href="#org376ee8c">1. Coding conventions</a>
<ul>
<li><a href="#orga29988b">1.1. Memory allocation</a></li>
<li><a href="#orgc73217c">1.1. Memory allocation</a></li>
</ul>
</li>
<li><a href="#org6d65809">2. Front end</a>
<li><a href="#org48ae4e5">2. Front end</a>
<ul>
<li><a href="#org3f51c78">2.1. Error handling</a>
<li><a href="#org07ec971">2.1. Error handling</a>
<ul>
<li><a href="#org6d78946">2.1.1. Decoding errors</a>
<li><a href="#org516f643">2.1.1. Decoding errors</a>
<ul>
<li><a href="#orgfe481b7">2.1.1.1. C source code</a></li>
<li><a href="#orgc0bbd34">2.1.1.2. Fortran interface</a></li>
<li><a href="#org40cd4d1">2.1.1.3. Python interface</a></li>
<li><a href="#org9d29258">2.1.1.1. C source code</a></li>
<li><a href="#org34ec8ac">2.1.1.2. Fortran interface</a></li>
<li><a href="#orgfe9432f">2.1.1.3. Python interface</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org0cb560b">2.2. Back ends</a>
<li><a href="#orgcffbb6e">2.2. Back ends</a>
<ul>
<li><a href="#org4176049">2.2.1. C</a></li>
<li><a href="#org0d24ea9">2.2.2. Fortran</a></li>
<li><a href="#org08d7364">2.2.3. Python</a></li>
<li><a href="#orgf2216fe">2.2.1. C</a></li>
<li><a href="#orgbbe364c">2.2.2. Fortran</a></li>
<li><a href="#orgb148faf">2.2.3. Python</a></li>
</ul>
</li>
<li><a href="#org1039f68">2.3. Read/write behavior</a></li>
<li><a href="#orgd0e1b37">2.4. TREXIO file type</a>
<li><a href="#org74cbea5">2.3. Read/write behavior</a></li>
<li><a href="#org1594cc1">2.4. TREXIO file type</a>
<ul>
<li><a href="#org3f19ed2">2.4.1. TREXIO<sub>File</sub> Python class</a></li>
<li><a href="#orgf132b0c">2.4.1. TREXIO<sub>File</sub> Python class</a></li>
</ul>
</li>
<li><a href="#org9d103df">2.5. Polymorphism of the file handle</a></li>
<li><a href="#org855a482">2.6. File opening</a>
<li><a href="#org4538535">2.5. Polymorphism of the file handle</a></li>
<li><a href="#org995fc86">2.6. File opening</a>
<ul>
<li><a href="#org877c568">2.6.1. C</a></li>
<li><a href="#org704f1fb">2.6.2. Fortran</a></li>
<li><a href="#orga1bd242">2.6.3. Python</a></li>
<li><a href="#orgc600c47">2.6.4. Zero-based versus one-based arrays of indices</a></li>
<li><a href="#org794ad4c">2.6.1. C</a></li>
<li><a href="#org63b30b0">2.6.2. Fortran</a></li>
<li><a href="#orgf14fbd1">2.6.3. Python</a></li>
<li><a href="#org52a1c71">2.6.4. Zero-based versus one-based arrays of indices</a></li>
</ul>
</li>
<li><a href="#orgd5053ed">2.7. File closing</a>
<li><a href="#org4f4019c">2.7. File closing</a>
<ul>
<li><a href="#org6dd25e6">2.7.1. C</a></li>
<li><a href="#orgae99e4b">2.7.2. Fortran</a></li>
<li><a href="#org397e967">2.7.3. Python</a></li>
<li><a href="#org13a171c">2.7.1. C</a></li>
<li><a href="#org4d91ea1">2.7.2. Fortran</a></li>
<li><a href="#org275c09f">2.7.3. Python</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgc9cf295">3. Templates for front end</a>
<li><a href="#orgb64fc80">3. Templates for front end</a>
<ul>
<li><a href="#org80f6482">3.1. Description</a></li>
<li><a href="#org5f19b1f">3.2. Templates for front end has/read/write a single numerical attribute</a>
<li><a href="#orga05f6f8">3.1. Description</a></li>
<li><a href="#org48a280d">3.2. Templates for front end has/read/write a single numerical attribute</a>
<ul>
<li><a href="#org939f045">3.2.1. Introduction</a></li>
<li><a href="#org50552af">3.2.2. C templates for front end</a>
<li><a href="#org314bbc3">3.2.1. Introduction</a></li>
<li><a href="#org5a5d11e">3.2.2. C templates for front end</a>
<ul>
<li><a href="#orgf561b12">3.2.2.1. Function declarations</a></li>
<li><a href="#orgc963541">3.2.2.2. Source code for double precision functions</a></li>
<li><a href="#org6c066bb">3.2.2.3. Source code for single precision functions</a></li>
<li><a href="#org6cf7937">3.2.2.4. Source code for default functions</a></li>
<li><a href="#org4ad78fe">3.2.2.1. Function declarations</a></li>
<li><a href="#orgb586ad1">3.2.2.2. Source code for double precision functions</a></li>
<li><a href="#org6251eb3">3.2.2.3. Source code for single precision functions</a></li>
<li><a href="#org60a2251">3.2.2.4. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#org9a40037">3.2.3. Fortran templates for front end</a></li>
<li><a href="#org7ea777a">3.2.4. Python templates for front end</a></li>
<li><a href="#org90c71b5">3.2.3. Fortran templates for front end</a></li>
<li><a href="#org6a33d39">3.2.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#org75cb8fd">3.3. Templates for front end has/read/write a dataset of numerical data</a>
<li><a href="#org15af64d">3.3. Templates for front end has/read/write a dataset of numerical data</a>
<ul>
<li><a href="#org6a86c77">3.3.1. Introduction</a></li>
<li><a href="#org7995460">3.3.2. C templates for front end</a>
<li><a href="#org098b96b">3.3.1. Introduction</a></li>
<li><a href="#org3d5aa09">3.3.2. C templates for front end</a>
<ul>
<li><a href="#orgc16256d">3.3.2.1. Function declarations</a></li>
<li><a href="#org7d5fb95">3.3.2.2. Source code for double precision functions</a></li>
<li><a href="#orgb4481bd">3.3.2.3. Source code for single precision functions</a></li>
<li><a href="#orgc53c702">3.3.2.4. Source code for memory-safe functions</a></li>
<li><a href="#org3233da0">3.3.2.5. Source code for default functions</a></li>
<li><a href="#org7f4342b">3.3.2.1. Function declarations</a></li>
<li><a href="#orgb180512">3.3.2.2. Source code for double precision functions</a></li>
<li><a href="#orge088cff">3.3.2.3. Source code for single precision functions</a></li>
<li><a href="#org32d9483">3.3.2.4. Source code for memory-safe functions</a></li>
<li><a href="#org3d25e1a">3.3.2.5. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#orgd35b657">3.3.3. Fortran templates for front end</a></li>
<li><a href="#org2d5a7b1">3.3.4. Python templates for front end</a></li>
<li><a href="#orgeeba40f">3.3.3. Fortran templates for front end</a></li>
<li><a href="#org9471f82">3.3.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#org5bf7e26">3.4. Sparse data structures</a></li>
<li><a href="#orgba88ff0">3.5. Templates for front end has/read/write a dataset of strings</a>
<li><a href="#org4a22be9">3.4. Sparse data structures</a></li>
<li><a href="#org20a9591">3.5. Templates for front end has/read/write a dataset of strings</a>
<ul>
<li><a href="#org46dc1b8">3.5.1. Introduction</a></li>
<li><a href="#org70d1119">3.5.2. C templates for front end</a>
<li><a href="#orgac06895">3.5.1. Introduction</a></li>
<li><a href="#orgf3e0ec3">3.5.2. C templates for front end</a>
<ul>
<li><a href="#orgdcdd9cb">3.5.2.1. Function declarations</a></li>
<li><a href="#orgf82cf7f">3.5.2.2. Source code for default functions</a></li>
<li><a href="#org39b9701">3.5.2.1. Function declarations</a></li>
<li><a href="#orgff3839d">3.5.2.2. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#orgedee2e5">3.5.3. Fortran templates for front end</a></li>
<li><a href="#org78926b2">3.5.4. Python templates for front end</a></li>
<li><a href="#org6f7563c">3.5.3. Fortran templates for front end</a></li>
<li><a href="#org11b97b3">3.5.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#org46ad0f6">3.6. Templates for front end has/read/write a single string attribute</a>
<li><a href="#orgff1970b">3.6. Templates for front end has/read/write a single string attribute</a>
<ul>
<li><a href="#orge8d4ce0">3.6.1. Introduction</a></li>
<li><a href="#org747cee1">3.6.2. C templates for front end</a>
<li><a href="#org51f58d5">3.6.1. Introduction</a></li>
<li><a href="#org4cfcd96">3.6.2. C templates for front end</a>
<ul>
<li><a href="#org9d6776c">3.6.2.1. Function declarations</a></li>
<li><a href="#org8ec874b">3.6.2.2. Source code for default functions</a></li>
<li><a href="#org2e7c209">3.6.2.1. Function declarations</a></li>
<li><a href="#orgc527d1e">3.6.2.2. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#org272d73f">3.6.3. Fortran templates for front end</a></li>
<li><a href="#org3bd04ca">3.6.4. Python templates for front end</a></li>
<li><a href="#org260f37c">3.6.3. Fortran templates for front end</a></li>
<li><a href="#orgaa16bd7">3.6.4. Python templates for front end</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgd568f3c">4. Fortran helper/wrapper functions</a></li>
<li><a href="#org890cf40">4. Fortran helper/wrapper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-org1e9450f" class="outline-2">
<h2 id="org1e9450f"><span class="section-number-2">1</span> Coding conventions</h2>
<div id="outline-container-org376ee8c" class="outline-2">
<h2 id="org376ee8c"><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>
@ -472,8 +472,8 @@ for the JavaScript code in this tag.
</ul>
</div>
<div id="outline-container-orga29988b" class="outline-3">
<h3 id="orga29988b"><span class="section-number-3">1.1</span> Memory allocation</h3>
<div id="outline-container-orgc73217c" class="outline-3">
<h3 id="orgc73217c"><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
@ -508,8 +508,8 @@ The maximum string size for the filenames is 4096 characters.
</div>
</div>
<div id="outline-container-org6d65809" class="outline-2">
<h2 id="org6d65809"><span class="section-number-2">2</span> Front end</h2>
<div id="outline-container-org48ae4e5" class="outline-2">
<h2 id="org48ae4e5"><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.
@ -517,10 +517,10 @@ TREXIO front end is modular, which simplifies implementation of new back ends.
</p>
</div>
<div id="outline-container-org3f51c78" class="outline-3">
<h3 id="org3f51c78"><span class="section-number-3">2.1</span> Error handling</h3>
<div id="outline-container-org07ec971" class="outline-3">
<h3 id="org07ec971"><span class="section-number-3">2.1</span> Error handling</h3>
<div class="outline-text-3" id="text-2-1">
<table id="org7932333" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org658bd6e" 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-org6d78946" class="outline-4">
<h4 id="org6d78946"><span class="section-number-4">2.1.1</span> Decoding errors</h4>
<div id="outline-container-org516f643" class="outline-4">
<h4 id="org516f643"><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-orgfe481b7" class="outline-5">
<h5 id="orgfe481b7"><span class="section-number-5">2.1.1.1</span> C source code</h5>
<div id="outline-container-org9d29258" class="outline-5">
<h5 id="org9d29258"><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>*
@ -872,8 +872,8 @@ The text strings are extracted from the previous table.
</div>
</div>
<div id="outline-container-orgc0bbd34" class="outline-5">
<h5 id="orgc0bbd34"><span class="section-number-5">2.1.1.2</span> Fortran interface</h5>
<div id="outline-container-org34ec8ac" class="outline-5">
<h5 id="org34ec8ac"><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>
@ -889,8 +889,8 @@ The text strings are extracted from the previous table.
</div>
</div>
<div id="outline-container-org40cd4d1" class="outline-5">
<h5 id="org40cd4d1"><span class="section-number-5">2.1.1.3</span> Python interface</h5>
<div id="outline-container-orgfe9432f" class="outline-5">
<h5 id="orgfe9432f"><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>):
@ -929,8 +929,8 @@ The text strings are extracted from the previous table.
</div>
</div>
<div id="outline-container-org0cb560b" class="outline-3">
<h3 id="org0cb560b"><span class="section-number-3">2.2</span> Back ends</h3>
<div id="outline-container-orgcffbb6e" class="outline-3">
<h3 id="orgcffbb6e"><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:
@ -954,8 +954,8 @@ lines that correspond to the <code>TREXIO_JSON</code> back end (not implemented
</p>
</div>
<div id="outline-container-org4176049" class="outline-4">
<h4 id="org4176049"><span class="section-number-4">2.2.1</span> C</h4>
<div id="outline-container-orgf2216fe" class="outline-4">
<h4 id="orgf2216fe"><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>;
@ -971,8 +971,8 @@ lines that correspond to the <code>TREXIO_JSON</code> back end (not implemented
</div>
</div>
<div id="outline-container-org0d24ea9" class="outline-4">
<h4 id="org0d24ea9"><span class="section-number-4">2.2.2</span> Fortran</h4>
<div id="outline-container-orgbbe364c" class="outline-4">
<h4 id="orgbbe364c"><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>
@ -984,8 +984,8 @@ lines that correspond to the <code>TREXIO_JSON</code> back end (not implemented
</div>
</div>
<div id="outline-container-org08d7364" class="outline-4">
<h4 id="org08d7364"><span class="section-number-4">2.2.3</span> Python</h4>
<div id="outline-container-orgb148faf" class="outline-4">
<h4 id="orgb148faf"><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>
@ -999,8 +999,8 @@ lines that correspond to the <code>TREXIO_JSON</code> back end (not implemented
</div>
</div>
<div id="outline-container-org1039f68" class="outline-3">
<h3 id="org1039f68"><span class="section-number-3">2.3</span> Read/write behavior</h3>
<div id="outline-container-org74cbea5" class="outline-3">
<h3 id="org74cbea5"><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
@ -1028,8 +1028,8 @@ concurrent programs, the behavior is not specified.
</p>
</div>
</div>
<div id="outline-container-orgd0e1b37" class="outline-3">
<h3 id="orgd0e1b37"><span class="section-number-3">2.4</span> TREXIO file type</h3>
<div id="outline-container-org1594cc1" class="outline-3">
<h3 id="org1594cc1"><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
@ -1063,8 +1063,8 @@ TREXIO files will have as a first argument the TREXIO file handle.
</div>
</div>
<div id="outline-container-org3f19ed2" class="outline-4">
<h4 id="org3f19ed2"><span class="section-number-4">2.4.1</span> TREXIO<sub>File</sub> Python class</h4>
<div id="outline-container-orgf132b0c" class="outline-4">
<h4 id="orgf132b0c"><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>:
@ -1137,8 +1137,8 @@ TREXIO files will have as a first argument the TREXIO file handle.
</div>
</div>
<div id="outline-container-org9d103df" class="outline-3">
<h3 id="org9d103df"><span class="section-number-3">2.5</span> Polymorphism of the file handle</h3>
<div id="outline-container-org4538535" class="outline-3">
<h3 id="org4538535"><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
@ -1157,8 +1157,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org855a482" class="outline-3">
<h3 id="org855a482"><span class="section-number-3">2.6</span> File opening</h3>
<div id="outline-container-org995fc86" class="outline-3">
<h3 id="org995fc86"><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.
@ -1197,8 +1197,8 @@ renaming the <code>.txt</code> data files.
</p>
</div>
<div id="outline-container-org877c568" class="outline-4">
<h4 id="org877c568"><span class="section-number-4">2.6.1</span> C</h4>
<div id="outline-container-org794ad4c" class="outline-4">
<h4 id="org794ad4c"><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>*
@ -1365,8 +1365,8 @@ renaming the <code>.txt</code> data files.
</div>
</div>
<div id="outline-container-org704f1fb" class="outline-4">
<h4 id="org704f1fb"><span class="section-number-4">2.6.2</span> Fortran</h4>
<div id="outline-container-org63b30b0" class="outline-4">
<h4 id="org63b30b0"><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>
@ -1384,8 +1384,8 @@ renaming the <code>.txt</code> data files.
</div>
</div>
<div id="outline-container-orga1bd242" class="outline-4">
<h4 id="orga1bd242"><span class="section-number-4">2.6.3</span> Python</h4>
<div id="outline-container-orgf14fbd1" class="outline-4">
<h4 id="orgf14fbd1"><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>):
@ -1433,8 +1433,8 @@ renaming the <code>.txt</code> data files.
</div>
</div>
<div id="outline-container-orgc600c47" class="outline-4">
<h4 id="orgc600c47"><span class="section-number-4">2.6.4</span> Zero-based versus one-based arrays of indices</h4>
<div id="outline-container-org52a1c71" class="outline-4">
<h4 id="org52a1c71"><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
@ -1467,8 +1467,8 @@ know if we need to shift by 1 arrays of indices.
</div>
</div>
<div id="outline-container-orgd5053ed" class="outline-3">
<h3 id="orgd5053ed"><span class="section-number-3">2.7</span> File closing</h3>
<div id="outline-container-org4f4019c" class="outline-3">
<h3 id="org4f4019c"><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.
@ -1485,8 +1485,8 @@ output:
</p>
</div>
<div id="outline-container-org6dd25e6" class="outline-4">
<h4 id="org6dd25e6"><span class="section-number-4">2.7.1</span> C</h4>
<div id="outline-container-org13a171c" class="outline-4">
<h4 id="org13a171c"><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>
@ -1557,8 +1557,8 @@ output:
</div>
</div>
<div id="outline-container-orgae99e4b" class="outline-4">
<h4 id="orgae99e4b"><span class="section-number-4">2.7.2</span> Fortran</h4>
<div id="outline-container-org4d91ea1" class="outline-4">
<h4 id="org4d91ea1"><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>
@ -1572,8 +1572,8 @@ output:
</div>
</div>
<div id="outline-container-org397e967" class="outline-4">
<h4 id="org397e967"><span class="section-number-4">2.7.3</span> Python</h4>
<div id="outline-container-org275c09f" class="outline-4">
<h4 id="org275c09f"><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):
@ -1595,12 +1595,12 @@ output:
</div>
</div>
<div id="outline-container-orgc9cf295" class="outline-2">
<h2 id="orgc9cf295"><span class="section-number-2">3</span> Templates for front end</h2>
<div id="outline-container-orgb64fc80" class="outline-2">
<h2 id="orgb64fc80"><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-org80f6482" class="outline-3">
<h3 id="org80f6482"><span class="section-number-3">3.1</span> Description</h3>
<div id="outline-container-orga05f6f8" class="outline-3">
<h3 id="orga05f6f8"><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>:
@ -1821,12 +1821,12 @@ value will result in <code>TREXIO_INVALID_ARG_2</code> exit code.
</div>
</div>
<div id="outline-container-org5f19b1f" class="outline-3">
<h3 id="org5f19b1f"><span class="section-number-3">3.2</span> Templates for front end has/read/write a single numerical attribute</h3>
<div id="outline-container-org48a280d" class="outline-3">
<h3 id="org48a280d"><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-org939f045" class="outline-4">
<h4 id="org939f045"><span class="section-number-4">3.2.1</span> Introduction</h4>
<div id="outline-container-org314bbc3" class="outline-4">
<h4 id="org314bbc3"><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,
@ -1897,8 +1897,8 @@ namely single value of int/float types.
</div>
</div>
<div id="outline-container-org50552af" class="outline-4">
<h4 id="org50552af"><span class="section-number-4">3.2.2</span> C templates for front end</h4>
<div id="outline-container-org5a5d11e" class="outline-4">
<h4 id="org5a5d11e"><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
@ -1912,12 +1912,12 @@ precision (see Table above).
</p>
</div>
<div id="outline-container-orgf561b12" class="outline-5">
<h5 id="orgf561b12"><span class="section-number-5">3.2.2.1</span> Function declarations</h5>
<div id="outline-container-org4ad78fe" class="outline-5">
<h5 id="org4ad78fe"><span class="section-number-5">3.2.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-orgc963541" class="outline-5">
<h5 id="orgc963541"><span class="section-number-5">3.2.2.2</span> Source code for double precision functions</h5>
<div id="outline-container-orgb586ad1" class="outline-5">
<h5 id="orgb586ad1"><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>
@ -1978,8 +1978,8 @@ precision (see Table above).
</div>
</div>
<div id="outline-container-org6c066bb" class="outline-5">
<h5 id="org6c066bb"><span class="section-number-5">3.2.2.3</span> Source code for single precision functions</h5>
<div id="outline-container-org6251eb3" class="outline-5">
<h5 id="org6251eb3"><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>
@ -2047,8 +2047,8 @@ precision (see Table above).
</div>
</div>
<div id="outline-container-org6cf7937" class="outline-5">
<h5 id="org6cf7937"><span class="section-number-5">3.2.2.4</span> Source code for default functions</h5>
<div id="outline-container-org60a2251" class="outline-5">
<h5 id="org60a2251"><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>
@ -2101,8 +2101,8 @@ precision (see Table above).
</div>
</div>
<div id="outline-container-org9a40037" class="outline-4">
<h4 id="org9a40037"><span class="section-number-4">3.2.3</span> Fortran templates for front end</h4>
<div id="outline-container-org90c71b5" class="outline-4">
<h4 id="org90c71b5"><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.
@ -2187,8 +2187,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-org7ea777a" class="outline-4">
<h4 id="org7ea777a"><span class="section-number-4">3.2.4</span> Python templates for front end</h4>
<div id="outline-container-org6a33d39" class="outline-4">
<h4 id="org6a33d39"><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>:
@ -2273,12 +2273,12 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-org75cb8fd" class="outline-3">
<h3 id="org75cb8fd"><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-org15af64d" class="outline-3">
<h3 id="org15af64d"><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-org6a86c77" class="outline-4">
<h4 id="org6a86c77"><span class="section-number-4">3.3.1</span> Introduction</h4>
<div id="outline-container-org098b96b" class="outline-4">
<h4 id="org098b96b"><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.
@ -2360,8 +2360,8 @@ This section concerns API calls related to datasets.
</div>
</div>
<div id="outline-container-org7995460" class="outline-4">
<h4 id="org7995460"><span class="section-number-4">3.3.2</span> C templates for front end</h4>
<div id="outline-container-org3d5aa09" class="outline-4">
<h4 id="org3d5aa09"><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.
@ -2372,13 +2372,13 @@ The basic (non-suffixed) API call on datasets deals with double precision (see T
</p>
</div>
<div id="outline-container-orgc16256d" class="outline-5">
<h5 id="orgc16256d"><span class="section-number-5">3.3.2.1</span> Function declarations</h5>
<div id="outline-container-org7f4342b" class="outline-5">
<h5 id="org7f4342b"><span class="section-number-5">3.3.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-org7d5fb95" class="outline-5">
<h5 id="org7d5fb95"><span class="section-number-5">3.3.2.2</span> Source code for double precision functions</h5>
<div id="outline-container-orgb180512" class="outline-5">
<h5 id="orgb180512"><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>
@ -2506,8 +2506,8 @@ The basic (non-suffixed) API call on datasets deals with double precision (see T
</div>
</div>
<div id="outline-container-orgb4481bd" class="outline-5">
<h5 id="orgb4481bd"><span class="section-number-5">3.3.2.3</span> Source code for single precision functions</h5>
<div id="outline-container-orge088cff" class="outline-5">
<h5 id="orge088cff"><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>
@ -2648,11 +2648,11 @@ The basic (non-suffixed) API call on datasets deals with double precision (see T
</div>
</div>
<div id="outline-container-orgc53c702" class="outline-5">
<h5 id="orgc53c702"><span class="section-number-5">3.3.2.4</span> Source code for memory-safe functions</h5>
<div id="outline-container-org32d9483" class="outline-5">
<h5 id="org32d9483"><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="org5e1bc0d"><span style="color: #228b22;">trexio_exit_code</span> <span style="color: #a0522d;">rc</span>;
<pre class="src src-c" id="orga35853e"><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>*/
@ -2808,8 +2808,8 @@ rc = trexio_read_$group_dset_dim$_64(file, &amp;($group_dset_dim$));
</div>
</div>
<div id="outline-container-org3233da0" class="outline-5">
<h5 id="org3233da0"><span class="section-number-5">3.3.2.5</span> Source code for default functions</h5>
<div id="outline-container-org3d25e1a" class="outline-5">
<h5 id="org3d25e1a"><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>
@ -2883,8 +2883,8 @@ rc = trexio_read_$group_dset_dim$_64(file, &amp;($group_dset_dim$));
</div>
</div>
<div id="outline-container-orgd35b657" class="outline-4">
<h4 id="orgd35b657"><span class="section-number-4">3.3.3</span> Fortran templates for front end</h4>
<div id="outline-container-orgeeba40f" class="outline-4">
<h4 id="orgeeba40f"><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>.
@ -2969,8 +2969,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-org2d5a7b1" class="outline-4">
<h4 id="org2d5a7b1"><span class="section-number-4">3.3.4</span> Python templates for front end</h4>
<div id="outline-container-org9471f82" class="outline-4">
<h4 id="org9471f82"><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>:
@ -3165,8 +3165,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-org5bf7e26" class="outline-3">
<h3 id="org5bf7e26"><span class="section-number-3">3.4</span> Sparse data structures</h3>
<div id="outline-container-org4a22be9" class="outline-3">
<h3 id="org4a22be9"><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
@ -3307,12 +3307,12 @@ For the values,
</div>
</div>
<div id="outline-container-orgba88ff0" class="outline-3">
<h3 id="orgba88ff0"><span class="section-number-3">3.5</span> Templates for front end has/read/write a dataset of strings</h3>
<div id="outline-container-org20a9591" class="outline-3">
<h3 id="org20a9591"><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-org46dc1b8" class="outline-4">
<h4 id="org46dc1b8"><span class="section-number-4">3.5.1</span> Introduction</h4>
<div id="outline-container-orgac06895" class="outline-4">
<h4 id="orgac06895"><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.
@ -3352,8 +3352,8 @@ This section concerns API calls related to datasets of strings.
</div>
</div>
<div id="outline-container-org70d1119" class="outline-4">
<h4 id="org70d1119"><span class="section-number-4">3.5.2</span> C templates for front end</h4>
<div id="outline-container-orgf3e0ec3" class="outline-4">
<h4 id="orgf3e0ec3"><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
@ -3361,12 +3361,12 @@ to/from the <code>TREXIO</code> file (except for <code>trexio_has_</code> functi
</p>
</div>
<div id="outline-container-orgdcdd9cb" class="outline-5">
<h5 id="orgdcdd9cb"><span class="section-number-5">3.5.2.1</span> Function declarations</h5>
<div id="outline-container-org39b9701" class="outline-5">
<h5 id="org39b9701"><span class="section-number-5">3.5.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-orgf82cf7f" class="outline-5">
<h5 id="orgf82cf7f"><span class="section-number-5">3.5.2.2</span> Source code for default functions</h5>
<div id="outline-container-orgff3839d" class="outline-5">
<h5 id="orgff3839d"><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>
@ -3608,8 +3608,8 @@ to/from the <code>TREXIO</code> file (except for <code>trexio_has_</code> functi
</div>
</div>
<div id="outline-container-orgedee2e5" class="outline-4">
<h4 id="orgedee2e5"><span class="section-number-4">3.5.3</span> Fortran templates for front end</h4>
<div id="outline-container-org6f7563c" class="outline-4">
<h4 id="org6f7563c"><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>.
@ -3705,8 +3705,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-org78926b2" class="outline-4">
<h4 id="org78926b2"><span class="section-number-4">3.5.4</span> Python templates for front end</h4>
<div id="outline-container-org11b97b3" class="outline-4">
<h4 id="org11b97b3"><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>:
@ -3822,12 +3822,12 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-org46ad0f6" class="outline-3">
<h3 id="org46ad0f6"><span class="section-number-3">3.6</span> Templates for front end has/read/write a single string attribute</h3>
<div id="outline-container-orgff1970b" class="outline-3">
<h3 id="orgff1970b"><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-orge8d4ce0" class="outline-4">
<h4 id="orge8d4ce0"><span class="section-number-4">3.6.1</span> Introduction</h4>
<div id="outline-container-org51f58d5" class="outline-4">
<h4 id="org51f58d5"><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.
@ -3867,16 +3867,16 @@ This section concerns API calls related to string attributes.
</div>
</div>
<div id="outline-container-org747cee1" class="outline-4">
<h4 id="org747cee1"><span class="section-number-4">3.6.2</span> C templates for front end</h4>
<div id="outline-container-org4cfcd96" class="outline-4">
<h4 id="org4cfcd96"><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-org9d6776c" class="outline-5">
<h5 id="org9d6776c"><span class="section-number-5">3.6.2.1</span> Function declarations</h5>
<div id="outline-container-org2e7c209" class="outline-5">
<h5 id="org2e7c209"><span class="section-number-5">3.6.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-org8ec874b" class="outline-5">
<h5 id="org8ec874b"><span class="section-number-5">3.6.2.2</span> Source code for default functions</h5>
<div id="outline-container-orgc527d1e" class="outline-5">
<h5 id="orgc527d1e"><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>
@ -3976,8 +3976,8 @@ This section concerns API calls related to string attributes.
</div>
</div>
<div id="outline-container-org272d73f" class="outline-4">
<h4 id="org272d73f"><span class="section-number-4">3.6.3</span> Fortran templates for front end</h4>
<div id="outline-container-org260f37c" class="outline-4">
<h4 id="org260f37c"><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.
@ -4054,8 +4054,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-org3bd04ca" class="outline-4">
<h4 id="org3bd04ca"><span class="section-number-4">3.6.4</span> Python templates for front end</h4>
<div id="outline-container-orgaa16bd7" class="outline-4">
<h4 id="orgaa16bd7"><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>:
@ -4145,8 +4145,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-orgd568f3c" class="outline-2">
<h2 id="orgd568f3c"><span class="section-number-2">4</span> Fortran helper/wrapper functions</h2>
<div id="outline-container-org890cf40" class="outline-2">
<h2 id="org890cf40"><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.
@ -4281,7 +4281,7 @@ 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: 2021-09-24 Fri 10:46</p>
<p class="date">Created: 2021-09-30 Thu 19:47</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

52
templator_hdf5.html
View File

@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2021-09-24 Fri 10:46 -->
<!-- 2021-09-30 Thu 19:47 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>HDF5 back end</title>
@ -317,27 +317,27 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org4e238ff">1. HDF5 back end</a>
<li><a href="#orge2c256b">1. HDF5 back end</a>
<ul>
<li><a href="#org1902d20">1.1. Template for HDF5 definitions</a></li>
<li><a href="#org8194f10">1.2. Template for HDF5 structures</a></li>
<li><a href="#orgb28f387">1.3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgfaa8c6b">1.4. Template for HDF5 has/read/write the numerical attribute</a></li>
<li><a href="#org8d8067d">1.5. Template for HDF5 has/read/write the dataset of numerical data</a></li>
<li><a href="#org7989e0b">1.6. Template for HDF5 has/read/write the dataset of strings</a></li>
<li><a href="#orgb4e071a">1.7. Template for HDF5 has/read/write the string attribute</a></li>
<li><a href="#org5417953">1.1. Template for HDF5 definitions</a></li>
<li><a href="#org1eaa4f8">1.2. Template for HDF5 structures</a></li>
<li><a href="#org84513d4">1.3. Template for HDF5 init/deinit</a></li>
<li><a href="#org36091b6">1.4. Template for HDF5 has/read/write the numerical attribute</a></li>
<li><a href="#org7e40736">1.5. Template for HDF5 has/read/write the dataset of numerical data</a></li>
<li><a href="#org3632620">1.6. Template for HDF5 has/read/write the dataset of strings</a></li>
<li><a href="#org27566b7">1.7. Template for HDF5 has/read/write the string attribute</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org4e238ff" class="outline-2">
<h2 id="org4e238ff"><span class="section-number-2">1</span> HDF5 back end</h2>
<div id="outline-container-orge2c256b" class="outline-2">
<h2 id="orge2c256b"><span class="section-number-2">1</span> HDF5 back end</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-org1902d20" class="outline-3">
<h3 id="org1902d20"><span class="section-number-3">1.1</span> Template for HDF5 definitions</h3>
<div id="outline-container-org5417953" class="outline-3">
<h3 id="org5417953"><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>
@ -349,8 +349,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org8194f10" class="outline-3">
<h3 id="org8194f10"><span class="section-number-3">1.2</span> Template for HDF5 structures</h3>
<div id="outline-container-org1eaa4f8" class="outline-3">
<h3 id="org1eaa4f8"><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> {
@ -364,8 +364,8 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-orgb28f387" class="outline-3">
<h3 id="orgb28f387"><span class="section-number-3">1.3</span> Template for HDF5 init/deinit</h3>
<div id="outline-container-org84513d4" class="outline-3">
<h3 id="org84513d4"><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>
@ -445,8 +445,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-orgfaa8c6b" class="outline-3">
<h3 id="orgfaa8c6b"><span class="section-number-3">1.4</span> Template for HDF5 has/read/write the numerical attribute</h3>
<div id="outline-container-org36091b6" class="outline-3">
<h3 id="org36091b6"><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>
@ -540,8 +540,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org8d8067d" class="outline-3">
<h3 id="org8d8067d"><span class="section-number-3">1.5</span> Template for HDF5 has/read/write the dataset of numerical data</h3>
<div id="outline-container-org7e40736" class="outline-3">
<h3 id="org7e40736"><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>
@ -664,8 +664,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org7989e0b" class="outline-3">
<h3 id="org7989e0b"><span class="section-number-3">1.6</span> Template for HDF5 has/read/write the dataset of strings</h3>
<div id="outline-container-org3632620" class="outline-3">
<h3 id="org3632620"><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>
@ -870,8 +870,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-orgb4e071a" class="outline-3">
<h3 id="orgb4e071a"><span class="section-number-3">1.7</span> Template for HDF5 has/read/write the string attribute</h3>
<div id="outline-container-org27566b7" class="outline-3">
<h3 id="org27566b7"><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>
@ -998,7 +998,7 @@ for the JavaScript code in this tag.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2021-09-24 Fri 10:46</p>
<p class="date">Created: 2021-09-30 Thu 19:47</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

112
templator_text.html
View File

@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2021-09-24 Fri 10:46 -->
<!-- 2021-09-30 Thu 19:47 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TEXT back end</title>
@ -317,26 +317,26 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org6948041">1. TEXT back end</a>
<li><a href="#org2bc3ad4">1. TEXT back end</a>
<ul>
<li><a href="#orgb3a4ee3">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#orga9c12f4">1.2. Template for general structure in text back end</a></li>
<li><a href="#org198bd3b">1.3. Initialize function (constant part)</a></li>
<li><a href="#org5f33f02">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#org3a85b88">1.5. Template for text read struct</a></li>
<li><a href="#orgb8d9b4b">1.6. Template for text flush struct</a></li>
<li><a href="#org820b858">1.7. Template for text free memory</a></li>
<li><a href="#org3b50558">1.8. Template for has/read/write the numerical attribute</a></li>
<li><a href="#orge0b0bc6">1.9. Template for has/read/write the dataset of numerical data</a></li>
<li><a href="#org2133a0e">1.10. Template for has/read/write the dataset of strings</a></li>
<li><a href="#org30e7044">1.11. Template for has/read/write the string attribute</a></li>
<li><a href="#org025af16">1.12. RDM struct (hard-coded)</a>
<li><a href="#org2378881">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#org6dc8d31">1.2. Template for general structure in text back end</a></li>
<li><a href="#orgd7c7a39">1.3. Initialize function (constant part)</a></li>
<li><a href="#orgbcde88c">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#org5ed3188">1.5. Template for text read struct</a></li>
<li><a href="#org4e13caa">1.6. Template for text flush struct</a></li>
<li><a href="#orgb89cc82">1.7. Template for text free memory</a></li>
<li><a href="#orgde1f115">1.8. Template for has/read/write the numerical attribute</a></li>
<li><a href="#org8e15dc1">1.9. Template for has/read/write the dataset of numerical data</a></li>
<li><a href="#orgcdea889">1.10. Template for has/read/write the dataset of strings</a></li>
<li><a href="#orgfc184e3">1.11. Template for has/read/write the string attribute</a></li>
<li><a href="#orgc9b00f5">1.12. RDM struct (hard-coded)</a>
<ul>
<li><a href="#org0f05042">1.12.1. Read the complete struct</a></li>
<li><a href="#org8705c1b">1.12.2. Flush the complete struct</a></li>
<li><a href="#orgbe964a5">1.12.3. Free memory</a></li>
<li><a href="#org74e392f">1.12.4. Read/Write the one<sub>e</sub> attribute</a></li>
<li><a href="#orged2ebb8">1.12.5. Read/Write the two<sub>e</sub> attribute</a></li>
<li><a href="#orga9016a5">1.12.1. Read the complete struct</a></li>
<li><a href="#orgb35e9fe">1.12.2. Flush the complete struct</a></li>
<li><a href="#org872ef09">1.12.3. Free memory</a></li>
<li><a href="#orgf842fc6">1.12.4. Read/Write the one<sub>e</sub> attribute</a></li>
<li><a href="#org2581fcd">1.12.5. Read/Write the two<sub>e</sub> attribute</a></li>
</ul>
</li>
</ul>
@ -345,8 +345,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org6948041" class="outline-2">
<h2 id="org6948041"><span class="section-number-2">1</span> TEXT back end</h2>
<div id="outline-container-org2bc3ad4" class="outline-2">
<h2 id="org2bc3ad4"><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
@ -367,8 +367,8 @@ The file is written when closed, or when the flush function is called.
</p>
</div>
<div id="outline-container-orgb3a4ee3" class="outline-3">
<h3 id="orgb3a4ee3"><span class="section-number-3">1.1</span> Template for group-related structures in text back end</h3>
<div id="outline-container-org2378881" class="outline-3">
<h3 id="org2378881"><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 {
@ -387,8 +387,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-orga9c12f4" class="outline-3">
<h3 id="orga9c12f4"><span class="section-number-3">1.2</span> Template for general structure in text back end</h3>
<div id="outline-container-org6dc8d31" class="outline-3">
<h3 id="org6dc8d31"><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> {
@ -414,8 +414,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-org198bd3b" class="outline-3">
<h3 id="org198bd3b"><span class="section-number-3">1.3</span> Initialize function (constant part)</h3>
<div id="outline-container-orgd7c7a39" class="outline-3">
<h3 id="orgd7c7a39"><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>
@ -516,8 +516,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-org5f33f02" class="outline-3">
<h3 id="org5f33f02"><span class="section-number-3">1.4</span> Deinitialize function (templated part)</h3>
<div id="outline-container-orgbcde88c" class="outline-3">
<h3 id="orgbcde88c"><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>
@ -542,8 +542,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-org3a85b88" class="outline-3">
<h3 id="org3a85b88"><span class="section-number-3">1.5</span> Template for text read struct</h3>
<div id="outline-container-org5ed3188" class="outline-3">
<h3 id="org5ed3188"><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*
@ -837,8 +837,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-orgb8d9b4b" class="outline-3">
<h3 id="orgb8d9b4b"><span class="section-number-3">1.6</span> Template for text flush struct</h3>
<div id="outline-container-org4e13caa" class="outline-3">
<h3 id="org4e13caa"><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>
@ -903,8 +903,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org820b858" class="outline-3">
<h3 id="org820b858"><span class="section-number-3">1.7</span> Template for text free memory</h3>
<div id="outline-container-orgb89cc82" class="outline-3">
<h3 id="orgb89cc82"><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.
@ -949,8 +949,8 @@ Memory is allocated when reading. The following function frees memory.
</div>
</div>
<div id="outline-container-org3b50558" class="outline-3">
<h3 id="org3b50558"><span class="section-number-3">1.8</span> Template for has/read/write the numerical attribute</h3>
<div id="outline-container-orgde1f115" class="outline-3">
<h3 id="orgde1f115"><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>
@ -1013,8 +1013,8 @@ Memory is allocated when reading. The following function frees memory.
</div>
</div>
<div id="outline-container-orge0b0bc6" class="outline-3">
<h3 id="orge0b0bc6"><span class="section-number-3">1.9</span> Template for has/read/write the dataset of numerical data</h3>
<div id="outline-container-org8e15dc1" class="outline-3">
<h3 id="org8e15dc1"><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.
@ -1110,8 +1110,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org2133a0e" class="outline-3">
<h3 id="org2133a0e"><span class="section-number-3">1.10</span> Template for has/read/write the dataset of strings</h3>
<div id="outline-container-orgcdea889" class="outline-3">
<h3 id="orgcdea889"><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.
@ -1212,8 +1212,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org30e7044" class="outline-3">
<h3 id="org30e7044"><span class="section-number-3">1.11</span> Template for has/read/write the string attribute</h3>
<div id="outline-container-orgfc184e3" class="outline-3">
<h3 id="orgfc184e3"><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>
@ -1287,12 +1287,12 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org025af16" class="outline-3">
<h3 id="org025af16"><span class="section-number-3">1.12</span> RDM struct (hard-coded)</h3>
<div id="outline-container-orgc9b00f5" class="outline-3">
<h3 id="orgc9b00f5"><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-org0f05042" class="outline-4">
<h4 id="org0f05042"><span class="section-number-4">1.12.1</span> Read the complete struct</h4>
<div id="outline-container-orga9016a5" class="outline-4">
<h4 id="orga9016a5"><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>);
@ -1387,8 +1387,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
<div id="outline-container-org8705c1b" class="outline-4">
<h4 id="org8705c1b"><span class="section-number-4">1.12.2</span> Flush the complete struct</h4>
<div id="outline-container-orgb35e9fe" class="outline-4">
<h4 id="orgb35e9fe"><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>);
@ -1430,8 +1430,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
<div id="outline-container-orgbe964a5" class="outline-4">
<h4 id="orgbe964a5"><span class="section-number-4">1.12.3</span> Free memory</h4>
<div id="outline-container-org872ef09" class="outline-4">
<h4 id="org872ef09"><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.
@ -1467,8 +1467,8 @@ Memory is allocated when reading. The followig function frees memory.
</div>
</div>
<div id="outline-container-org74e392f" class="outline-4">
<h4 id="org74e392f"><span class="section-number-4">1.12.4</span> Read/Write the one<sub>e</sub> attribute</h4>
<div id="outline-container-orgf842fc6" class="outline-4">
<h4 id="orgf842fc6"><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.
@ -1534,8 +1534,8 @@ The <code>one_e</code> array is assumed allocated with the appropriate size.
</div>
</div>
<div id="outline-container-orged2ebb8" class="outline-4">
<h4 id="orged2ebb8"><span class="section-number-4">1.12.5</span> Read/Write the two<sub>e</sub> attribute</h4>
<div id="outline-container-org2581fcd" class="outline-4">
<h4 id="org2581fcd"><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
@ -1643,7 +1643,7 @@ file for each sparse float structure.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2021-09-24 Fri 10:46</p>
<p class="date">Created: 2021-09-30 Thu 19:47</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

118
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>
<!-- 2021-09-24 Fri 10:46 -->
<!-- 2021-09-30 Thu 19:47 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREX Configuration file</title>
@ -339,28 +339,28 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orge071f03">1. Metadata (metadata group)</a></li>
<li><a href="#orga2ee45e">2. Electron (electron group)</a></li>
<li><a href="#org73882e0">3. Nucleus (nucleus group)</a></li>
<li><a href="#org7b7e7b5">4. Effective core potentials (ecp group)</a></li>
<li><a href="#org23b79ad">5. Basis set (basis group)</a></li>
<li><a href="#org73b83da">6. Atomic orbitals (ao group)</a>
<li><a href="#org6e55e02">1. Metadata (metadata group)</a></li>
<li><a href="#org9db995a">2. Electron (electron group)</a></li>
<li><a href="#org2ad13ed">3. Nucleus (nucleus group)</a></li>
<li><a href="#orgc63a65a">4. Effective core potentials (ecp group)</a></li>
<li><a href="#org9ef8385">5. Basis set (basis group)</a></li>
<li><a href="#org0d08cf0">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="#org06e53c5">7. Molecular orbitals (mo group)</a>
<li><a href="#orgb1e1923">7. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#orgdeb666d">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgc9ba12b">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org4b00d86">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgf9f46f2">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#org8c8ae43">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#org4b29da2">9. <span class="todo TODO">TODO</span> Reduced density matrices (rdm group)</a></li>
<li><a href="#org085bd0a">10. Appendix</a>
<li><a href="#org7dfa876">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#orgc21a6f0">9. <span class="todo TODO">TODO</span> Reduced density matrices (rdm group)</a></li>
<li><a href="#org30505a4">10. Appendix</a>
<ul>
<li><a href="#org6fe99d1">10.1. Python script from table to json</a></li>
<li><a href="#org039e88b">10.1. Python script from table to json</a></li>
</ul>
</li>
</ul>
@ -402,8 +402,8 @@ 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-orge071f03" class="outline-2">
<h2 id="orge071f03"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org6e55e02" class="outline-2">
<h2 id="org6e55e02"><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
@ -413,7 +413,7 @@ which have participated to the creation of the file, a list of
authors of the file, and a textual description.
</p>
<table id="orged3df0d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org7c48f01" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -480,15 +480,15 @@ authors of the file, and a textual description.
</div>
</div>
<div id="outline-container-orga2ee45e" class="outline-2">
<h2 id="orga2ee45e"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div id="outline-container-org9db995a" class="outline-2">
<h2 id="org9db995a"><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="org38267a6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgad0adca" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -527,15 +527,15 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-org73882e0" class="outline-2">
<h2 id="org73882e0"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div id="outline-container-org2ad13ed" class="outline-2">
<h2 id="org2ad13ed"><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="org323e615" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf4b81d7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -595,8 +595,8 @@ given in Cartesian \((x,y,z)\) format.
</div>
</div>
<div id="outline-container-org7b7e7b5" class="outline-2">
<h2 id="org7b7e7b5"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div id="outline-container-orgc63a65a" class="outline-2">
<h2 id="orgc63a65a"><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
@ -624,7 +624,7 @@ 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> for more info.
</p>
<table id="orge12c8a5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgdc45b88" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -733,8 +733,8 @@ See <a href="http://dx.doi.org/10.1063/1.4984046">http://dx.doi.org/10.1063/1.49
</div>
</div>
<div id="outline-container-org23b79ad" class="outline-2">
<h2 id="org23b79ad"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div id="outline-container-org9ef8385" class="outline-2">
<h2 id="org9ef8385"><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
@ -787,7 +787,7 @@ 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="org18b2d99" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgfa757ca" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -956,8 +956,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-org73b83da" class="outline-2">
<h2 id="org73b83da"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div id="outline-container-org0d08cf0" class="outline-2">
<h2 id="org0d08cf0"><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
@ -1005,13 +1005,13 @@ shell, as in the GAMESS convention where
<p>
In such a case, one should set the normalization of the shell (in
the <a href="#org23b79ad">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#org9ef8385">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="org32e547e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb6ad7aa" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1063,8 +1063,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
</table>
</div>
<div id="outline-container-org3d5d1ae" class="outline-3">
<h3 id="ao_one_e"><a id="org3d5d1ae"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div id="outline-container-orgac2f827" class="outline-3">
<h3 id="ao_one_e"><a id="orgac2f827"></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}}
@ -1082,7 +1082,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="org22d4741" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb6d23b6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1149,8 +1149,8 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org792b19c" class="outline-3">
<h3 id="ao_two_e"><a id="org792b19c"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div id="outline-container-orgf3037c7" class="outline-3">
<h3 id="ao_two_e"><a id="orgf3037c7"></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
@ -1171,7 +1171,7 @@ notation.
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
</ul>
<table id="org70941a0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb2b8ef3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1211,10 +1211,10 @@ notation.
</div>
</div>
<div id="outline-container-org06e53c5" class="outline-2">
<h2 id="org06e53c5"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div id="outline-container-orgb1e1923" class="outline-2">
<h2 id="orgb1e1923"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div class="outline-text-2" id="text-7">
<table id="org085f5b4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd30c679" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1280,8 +1280,8 @@ notation.
</table>
</div>
<div id="outline-container-orgdeb666d" class="outline-3">
<h3 id="orgdeb666d"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div id="outline-container-org4b00d86" class="outline-3">
<h3 id="org4b00d86"><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
@ -1289,7 +1289,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org787b1b6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org32c0e62" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1356,8 +1356,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-orgc9ba12b" class="outline-3">
<h3 id="orgc9ba12b"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div id="outline-container-orgf9f46f2" class="outline-3">
<h3 id="orgf9f46f2"><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
@ -1365,7 +1365,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org0903526" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org9e8f49b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1405,13 +1405,13 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org8c8ae43" class="outline-2">
<h2 id="org8c8ae43"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
<div id="outline-container-org7dfa876" class="outline-2">
<h2 id="org7dfa876"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
</div>
<div id="outline-container-org4b29da2" class="outline-2">
<h2 id="org4b29da2"><span class="section-number-2">9</span> <span class="todo TODO">TODO</span> Reduced density matrices (rdm group)</h2>
<div id="outline-container-orgc21a6f0" class="outline-2">
<h2 id="orgc21a6f0"><span class="section-number-2">9</span> <span class="todo TODO">TODO</span> Reduced density matrices (rdm group)</h2>
<div class="outline-text-2" id="text-9">
<table id="org5c4d9de" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge1c31de" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1464,15 +1464,15 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org085bd0a" class="outline-2">
<h2 id="org085bd0a"><span class="section-number-2">10</span> Appendix</h2>
<div id="outline-container-org30505a4" class="outline-2">
<h2 id="org30505a4"><span class="section-number-2">10</span> Appendix</h2>
<div class="outline-text-2" id="text-10">
</div>
<div id="outline-container-org6fe99d1" class="outline-3">
<h3 id="org6fe99d1"><span class="section-number-3">10.1</span> Python script from table to json</h3>
<div id="outline-container-org039e88b" class="outline-3">
<h3 id="org039e88b"><span class="section-number-3">10.1</span> Python script from table to json</h3>
<div class="outline-text-3" id="text-10-1">
<div class="org-src-container">
<pre class="src src-python" id="orgc7efb1a"><span style="color: #a020f0;">print</span>(<span style="color: #8b2252;">"""#+begin_src python :tangle trex.json"""</span>)
<pre class="src src-python" id="org5adfa72"><span style="color: #a020f0;">print</span>(<span style="color: #8b2252;">"""#+begin_src python :tangle trex.json"""</span>)
<span style="color: #a020f0;">print</span>(<span style="color: #8b2252;">""" "%s": {"""</span>%(title))
<span style="color: #a0522d;">indent</span> = <span style="color: #8b2252;">" "</span>
<span style="color: #a0522d;">f1</span> = 0 ; <span style="color: #a0522d;">f2</span> = 0 ; <span style="color: #a0522d;">f3</span> = 0
@ -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: 2021-09-24 Fri 10:46</p>
<p class="date">Created: 2021-09-30 Thu 19:47</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>