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README.html
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2021-11-17 Wed 13:18 -->
<!-- 2021-11-17 Wed 13:23 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title>
@ -343,7 +343,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2021-11-17 Wed 13:18</p>
<p class="date">Created: 2021-11-17 Wed 13:23</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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Sparse.html
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2021-11-17 Wed 13:18 -->
<!-- 2021-11-17 Wed 13:23 -->
<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="#org72a0023">1. Text back end</a></li>
<li><a href="#org19b0c52">2. HDF5 Back end</a></li>
<li><a href="#orgb5b4d33">1. Text back end</a></li>
<li><a href="#org70761b6">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-org72a0023" class="outline-2">
<h2 id="org72a0023"><span class="section-number-2">1</span> Text back end</h2>
<div id="outline-container-orgb5b4d33" class="outline-2">
<h2 id="orgb5b4d33"><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-org19b0c52" class="outline-2">
<h2 id="org19b0c52"><span class="section-number-2">2</span> HDF5 Back end</h2>
<div id="outline-container-org70761b6" class="outline-2">
<h2 id="org70761b6"><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: 2021-11-17 Wed 13:18</p>
<p class="date">Created: 2021-11-17 Wed 13:23</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>
<!-- 2021-11-17 Wed 13:18 -->
<!-- 2021-11-17 Wed 13:23 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title>
@ -343,7 +343,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2021-11-17 Wed 13:18</p>
<p class="date">Created: 2021-11-17 Wed 13:23</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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templator_front.html
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2021-11-17 Wed 13:18 -->
<!-- 2021-11-17 Wed 13:23 -->
<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="#orgf789848">1. Coding conventions</a>
<li><a href="#org7f654e5">1. Coding conventions</a>
<ul>
<li><a href="#org5dfbfc9">1.1. Memory allocation</a></li>
<li><a href="#org292264c">1.1. Memory allocation</a></li>
</ul>
</li>
<li><a href="#orgf16a786">2. Front end</a>
<li><a href="#org13ee678">2. Front end</a>
<ul>
<li><a href="#org0e0e1ad">2.1. Error handling</a>
<li><a href="#orgb675c96">2.1. Error handling</a>
<ul>
<li><a href="#orgcc88b17">2.1.1. Decoding errors</a>
<li><a href="#orgac5bb0a">2.1.1. Decoding errors</a>
<ul>
<li><a href="#org9e4ce1f">2.1.1.1. C source code</a></li>
<li><a href="#org236ed3b">2.1.1.2. Fortran interface</a></li>
<li><a href="#orgc312514">2.1.1.3. Python interface</a></li>
<li><a href="#orgb6bc083">2.1.1.1. C source code</a></li>
<li><a href="#org5e4725a">2.1.1.2. Fortran interface</a></li>
<li><a href="#orge1be896">2.1.1.3. Python interface</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org1ce805f">2.2. Back ends</a>
<li><a href="#org85dbb4a">2.2. Back ends</a>
<ul>
<li><a href="#orgd026f15">2.2.1. C</a></li>
<li><a href="#org69df03a">2.2.2. Fortran</a></li>
<li><a href="#org34c13ba">2.2.3. Python</a></li>
<li><a href="#org906f173">2.2.1. C</a></li>
<li><a href="#orga43b2fa">2.2.2. Fortran</a></li>
<li><a href="#org34ca8c3">2.2.3. Python</a></li>
</ul>
</li>
<li><a href="#orgc5e42c7">2.3. Read/write behavior</a></li>
<li><a href="#org491b545">2.4. TREXIO file type</a>
<li><a href="#org9a30fe5">2.3. Read/write behavior</a></li>
<li><a href="#org5bedf49">2.4. TREXIO file type</a>
<ul>
<li><a href="#org40ecde0">2.4.1. TREXIO<sub>File</sub> Python class</a></li>
<li><a href="#org0d9626e">2.4.1. TREXIO<sub>File</sub> Python class</a></li>
</ul>
</li>
<li><a href="#orgf5319ff">2.5. Polymorphism of the file handle</a></li>
<li><a href="#org430cb53">2.6. File opening</a>
<li><a href="#org6489bd9">2.5. Polymorphism of the file handle</a></li>
<li><a href="#orgffecd50">2.6. File opening</a>
<ul>
<li><a href="#orgc04db55">2.6.1. C</a></li>
<li><a href="#orgde42092">2.6.2. Fortran</a></li>
<li><a href="#org76230d7">2.6.3. Python</a></li>
<li><a href="#org5d6edaa">2.6.4. Zero-based versus one-based arrays of indices</a></li>
<li><a href="#org6e08a90">2.6.1. C</a></li>
<li><a href="#orga77331e">2.6.2. Fortran</a></li>
<li><a href="#org2c4cae7">2.6.3. Python</a></li>
<li><a href="#org28d80a7">2.6.4. Zero-based versus one-based arrays of indices</a></li>
</ul>
</li>
<li><a href="#org44f7c7a">2.7. File closing</a>
<li><a href="#orgce863b0">2.7. File closing</a>
<ul>
<li><a href="#orgdd7329a">2.7.1. C</a></li>
<li><a href="#orgeeb17c5">2.7.2. Fortran</a></li>
<li><a href="#orgffbb320">2.7.3. Python</a></li>
<li><a href="#org22bc414">2.7.1. C</a></li>
<li><a href="#org8019549">2.7.2. Fortran</a></li>
<li><a href="#orgb95a1ea">2.7.3. Python</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org0252c18">3. Templates for front end</a>
<li><a href="#orga081e91">3. Templates for front end</a>
<ul>
<li><a href="#org4f5e82f">3.1. Description</a></li>
<li><a href="#org165d32c">3.2. Templates for front end has/read/write a single numerical attribute</a>
<li><a href="#orgdd9c2fa">3.1. Description</a></li>
<li><a href="#orge6e2cf4">3.2. Templates for front end has/read/write a single numerical attribute</a>
<ul>
<li><a href="#orge193c1e">3.2.1. Introduction</a></li>
<li><a href="#orgc0a4b61">3.2.2. C templates for front end</a>
<li><a href="#org706c103">3.2.1. Introduction</a></li>
<li><a href="#org99db369">3.2.2. C templates for front end</a>
<ul>
<li><a href="#orgf05e356">3.2.2.1. Function declarations</a></li>
<li><a href="#org1cce195">3.2.2.2. Source code for double precision functions</a></li>
<li><a href="#orgdfdf73d">3.2.2.3. Source code for single precision functions</a></li>
<li><a href="#org4512700">3.2.2.4. Source code for default functions</a></li>
<li><a href="#orgb8fc317">3.2.2.1. Function declarations</a></li>
<li><a href="#orga4ed762">3.2.2.2. Source code for double precision functions</a></li>
<li><a href="#org8ec2c49">3.2.2.3. Source code for single precision functions</a></li>
<li><a href="#orge0352ce">3.2.2.4. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#org7f27069">3.2.3. Fortran templates for front end</a></li>
<li><a href="#org36d6039">3.2.4. Python templates for front end</a></li>
<li><a href="#org8e2a35b">3.2.3. Fortran templates for front end</a></li>
<li><a href="#org17690fb">3.2.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#org4d87892">3.3. Templates for front end has/read/write a dataset of numerical data</a>
<li><a href="#orga4e7942">3.3. Templates for front end has/read/write a dataset of numerical data</a>
<ul>
<li><a href="#org9875828">3.3.1. Introduction</a></li>
<li><a href="#orgf923ee8">3.3.2. C templates for front end</a>
<li><a href="#org9ee4c23">3.3.1. Introduction</a></li>
<li><a href="#orgd9c8dd3">3.3.2. C templates for front end</a>
<ul>
<li><a href="#orga9d3ee8">3.3.2.1. Function declarations</a></li>
<li><a href="#orgae612b7">3.3.2.2. Source code for double precision functions</a></li>
<li><a href="#orgacfd7ae">3.3.2.3. Source code for single precision functions</a></li>
<li><a href="#org06879f2">3.3.2.4. Source code for memory-safe functions</a></li>
<li><a href="#org32c325e">3.3.2.5. Source code for default functions</a></li>
<li><a href="#org0bab725">3.3.2.1. Function declarations</a></li>
<li><a href="#orgf30a05f">3.3.2.2. Source code for double precision functions</a></li>
<li><a href="#org76bbfe0">3.3.2.3. Source code for single precision functions</a></li>
<li><a href="#org76c152b">3.3.2.4. Source code for memory-safe functions</a></li>
<li><a href="#org7678f8f">3.3.2.5. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#org868cea9">3.3.3. Fortran templates for front end</a></li>
<li><a href="#org086e334">3.3.4. Python templates for front end</a></li>
<li><a href="#org37bd15c">3.3.3. Fortran templates for front end</a></li>
<li><a href="#org3a86462">3.3.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#org7bffb82">3.4. Sparse data structures</a></li>
<li><a href="#orga10aa96">3.5. Templates for front end has/read/write a dataset of strings</a>
<li><a href="#orge763eef">3.4. Sparse data structures</a></li>
<li><a href="#org41df8f6">3.5. Templates for front end has/read/write a dataset of strings</a>
<ul>
<li><a href="#org53d449d">3.5.1. Introduction</a></li>
<li><a href="#orgc24c4c7">3.5.2. C templates for front end</a>
<li><a href="#org2d52fef">3.5.1. Introduction</a></li>
<li><a href="#org63d2cab">3.5.2. C templates for front end</a>
<ul>
<li><a href="#org56f44a8">3.5.2.1. Function declarations</a></li>
<li><a href="#org1dc15fe">3.5.2.2. Source code for default functions</a></li>
<li><a href="#orgaf1e835">3.5.2.1. Function declarations</a></li>
<li><a href="#orgeff74dc">3.5.2.2. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#org6c39cea">3.5.3. Fortran templates for front end</a></li>
<li><a href="#org9e1fd4a">3.5.4. Python templates for front end</a></li>
<li><a href="#org4573f63">3.5.3. Fortran templates for front end</a></li>
<li><a href="#orgcdfb9e8">3.5.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#org2465a60">3.6. Templates for front end has/read/write a single string attribute</a>
<li><a href="#orgbb8712c">3.6. Templates for front end has/read/write a single string attribute</a>
<ul>
<li><a href="#org941f7fe">3.6.1. Introduction</a></li>
<li><a href="#orga68b075">3.6.2. C templates for front end</a>
<li><a href="#orga1f906e">3.6.1. Introduction</a></li>
<li><a href="#orge414cdd">3.6.2. C templates for front end</a>
<ul>
<li><a href="#org4950592">3.6.2.1. Function declarations</a></li>
<li><a href="#orgf608d87">3.6.2.2. Source code for default functions</a></li>
<li><a href="#org7275750">3.6.2.1. Function declarations</a></li>
<li><a href="#org74f3fd4">3.6.2.2. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#orgd6b81f1">3.6.3. Fortran templates for front end</a></li>
<li><a href="#org18811a1">3.6.4. Python templates for front end</a></li>
<li><a href="#org3348112">3.6.3. Fortran templates for front end</a></li>
<li><a href="#orge8583f1">3.6.4. Python templates for front end</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgff37ee5">4. Fortran helper/wrapper functions</a></li>
<li><a href="#org994aafe">4. Fortran helper/wrapper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-orgf789848" class="outline-2">
<h2 id="orgf789848"><span class="section-number-2">1</span> Coding conventions</h2>
<div id="outline-container-org7f654e5" class="outline-2">
<h2 id="org7f654e5"><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-org5dfbfc9" class="outline-3">
<h3 id="org5dfbfc9"><span class="section-number-3">1.1</span> Memory allocation</h3>
<div id="outline-container-org292264c" class="outline-3">
<h3 id="org292264c"><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-orgf16a786" class="outline-2">
<h2 id="orgf16a786"><span class="section-number-2">2</span> Front end</h2>
<div id="outline-container-org13ee678" class="outline-2">
<h2 id="org13ee678"><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-org0e0e1ad" class="outline-3">
<h3 id="org0e0e1ad"><span class="section-number-3">2.1</span> Error handling</h3>
<div id="outline-container-orgb675c96" class="outline-3">
<h3 id="orgb675c96"><span class="section-number-3">2.1</span> Error handling</h3>
<div class="outline-text-3" id="text-2-1">
<table id="org3463af9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org7fd5e61" 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-orgcc88b17" class="outline-4">
<h4 id="orgcc88b17"><span class="section-number-4">2.1.1</span> Decoding errors</h4>
<div id="outline-container-orgac5bb0a" class="outline-4">
<h4 id="orgac5bb0a"><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-org9e4ce1f" class="outline-5">
<h5 id="org9e4ce1f"><span class="section-number-5">2.1.1.1</span> C source code</h5>
<div id="outline-container-orgb6bc083" class="outline-5">
<h5 id="orgb6bc083"><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-org236ed3b" class="outline-5">
<h5 id="org236ed3b"><span class="section-number-5">2.1.1.2</span> Fortran interface</h5>
<div id="outline-container-org5e4725a" class="outline-5">
<h5 id="org5e4725a"><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-orgc312514" class="outline-5">
<h5 id="orgc312514"><span class="section-number-5">2.1.1.3</span> Python interface</h5>
<div id="outline-container-orge1be896" class="outline-5">
<h5 id="orge1be896"><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-org1ce805f" class="outline-3">
<h3 id="org1ce805f"><span class="section-number-3">2.2</span> Back ends</h3>
<div id="outline-container-org85dbb4a" class="outline-3">
<h3 id="org85dbb4a"><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-orgd026f15" class="outline-4">
<h4 id="orgd026f15"><span class="section-number-4">2.2.1</span> C</h4>
<div id="outline-container-org906f173" class="outline-4">
<h4 id="org906f173"><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-org69df03a" class="outline-4">
<h4 id="org69df03a"><span class="section-number-4">2.2.2</span> Fortran</h4>
<div id="outline-container-orga43b2fa" class="outline-4">
<h4 id="orga43b2fa"><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-org34c13ba" class="outline-4">
<h4 id="org34c13ba"><span class="section-number-4">2.2.3</span> Python</h4>
<div id="outline-container-org34ca8c3" class="outline-4">
<h4 id="org34ca8c3"><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-orgc5e42c7" class="outline-3">
<h3 id="orgc5e42c7"><span class="section-number-3">2.3</span> Read/write behavior</h3>
<div id="outline-container-org9a30fe5" class="outline-3">
<h3 id="org9a30fe5"><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-org491b545" class="outline-3">
<h3 id="org491b545"><span class="section-number-3">2.4</span> TREXIO file type</h3>
<div id="outline-container-org5bedf49" class="outline-3">
<h3 id="org5bedf49"><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-org40ecde0" class="outline-4">
<h4 id="org40ecde0"><span class="section-number-4">2.4.1</span> TREXIO<sub>File</sub> Python class</h4>
<div id="outline-container-org0d9626e" class="outline-4">
<h4 id="org0d9626e"><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-orgf5319ff" class="outline-3">
<h3 id="orgf5319ff"><span class="section-number-3">2.5</span> Polymorphism of the file handle</h3>
<div id="outline-container-org6489bd9" class="outline-3">
<h3 id="org6489bd9"><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-org430cb53" class="outline-3">
<h3 id="org430cb53"><span class="section-number-3">2.6</span> File opening</h3>
<div id="outline-container-orgffecd50" class="outline-3">
<h3 id="orgffecd50"><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-orgc04db55" class="outline-4">
<h4 id="orgc04db55"><span class="section-number-4">2.6.1</span> C</h4>
<div id="outline-container-org6e08a90" class="outline-4">
<h4 id="org6e08a90"><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-orgde42092" class="outline-4">
<h4 id="orgde42092"><span class="section-number-4">2.6.2</span> Fortran</h4>
<div id="outline-container-orga77331e" class="outline-4">
<h4 id="orga77331e"><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-org76230d7" class="outline-4">
<h4 id="org76230d7"><span class="section-number-4">2.6.3</span> Python</h4>
<div id="outline-container-org2c4cae7" class="outline-4">
<h4 id="org2c4cae7"><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-org5d6edaa" class="outline-4">
<h4 id="org5d6edaa"><span class="section-number-4">2.6.4</span> Zero-based versus one-based arrays of indices</h4>
<div id="outline-container-org28d80a7" class="outline-4">
<h4 id="org28d80a7"><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-org44f7c7a" class="outline-3">
<h3 id="org44f7c7a"><span class="section-number-3">2.7</span> File closing</h3>
<div id="outline-container-orgce863b0" class="outline-3">
<h3 id="orgce863b0"><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-orgdd7329a" class="outline-4">
<h4 id="orgdd7329a"><span class="section-number-4">2.7.1</span> C</h4>
<div id="outline-container-org22bc414" class="outline-4">
<h4 id="org22bc414"><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-orgeeb17c5" class="outline-4">
<h4 id="orgeeb17c5"><span class="section-number-4">2.7.2</span> Fortran</h4>
<div id="outline-container-org8019549" class="outline-4">
<h4 id="org8019549"><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-orgffbb320" class="outline-4">
<h4 id="orgffbb320"><span class="section-number-4">2.7.3</span> Python</h4>
<div id="outline-container-orgb95a1ea" class="outline-4">
<h4 id="orgb95a1ea"><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-org0252c18" class="outline-2">
<h2 id="org0252c18"><span class="section-number-2">3</span> Templates for front end</h2>
<div id="outline-container-orga081e91" class="outline-2">
<h2 id="orga081e91"><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-org4f5e82f" class="outline-3">
<h3 id="org4f5e82f"><span class="section-number-3">3.1</span> Description</h3>
<div id="outline-container-orgdd9c2fa" class="outline-3">
<h3 id="orgdd9c2fa"><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-org165d32c" class="outline-3">
<h3 id="org165d32c"><span class="section-number-3">3.2</span> Templates for front end has/read/write a single numerical attribute</h3>
<div id="outline-container-orge6e2cf4" class="outline-3">
<h3 id="orge6e2cf4"><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-orge193c1e" class="outline-4">
<h4 id="orge193c1e"><span class="section-number-4">3.2.1</span> Introduction</h4>
<div id="outline-container-org706c103" class="outline-4">
<h4 id="org706c103"><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-orgc0a4b61" class="outline-4">
<h4 id="orgc0a4b61"><span class="section-number-4">3.2.2</span> C templates for front end</h4>
<div id="outline-container-org99db369" class="outline-4">
<h4 id="org99db369"><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-orgf05e356" class="outline-5">
<h5 id="orgf05e356"><span class="section-number-5">3.2.2.1</span> Function declarations</h5>
<div id="outline-container-orgb8fc317" class="outline-5">
<h5 id="orgb8fc317"><span class="section-number-5">3.2.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-org1cce195" class="outline-5">
<h5 id="org1cce195"><span class="section-number-5">3.2.2.2</span> Source code for double precision functions</h5>
<div id="outline-container-orga4ed762" class="outline-5">
<h5 id="orga4ed762"><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-orgdfdf73d" class="outline-5">
<h5 id="orgdfdf73d"><span class="section-number-5">3.2.2.3</span> Source code for single precision functions</h5>
<div id="outline-container-org8ec2c49" class="outline-5">
<h5 id="org8ec2c49"><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-org4512700" class="outline-5">
<h5 id="org4512700"><span class="section-number-5">3.2.2.4</span> Source code for default functions</h5>
<div id="outline-container-orge0352ce" class="outline-5">
<h5 id="orge0352ce"><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-org7f27069" class="outline-4">
<h4 id="org7f27069"><span class="section-number-4">3.2.3</span> Fortran templates for front end</h4>
<div id="outline-container-org8e2a35b" class="outline-4">
<h4 id="org8e2a35b"><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-org36d6039" class="outline-4">
<h4 id="org36d6039"><span class="section-number-4">3.2.4</span> Python templates for front end</h4>
<div id="outline-container-org17690fb" class="outline-4">
<h4 id="org17690fb"><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-org4d87892" class="outline-3">
<h3 id="org4d87892"><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-orga4e7942" class="outline-3">
<h3 id="orga4e7942"><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-org9875828" class="outline-4">
<h4 id="org9875828"><span class="section-number-4">3.3.1</span> Introduction</h4>
<div id="outline-container-org9ee4c23" class="outline-4">
<h4 id="org9ee4c23"><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-orgf923ee8" class="outline-4">
<h4 id="orgf923ee8"><span class="section-number-4">3.3.2</span> C templates for front end</h4>
<div id="outline-container-orgd9c8dd3" class="outline-4">
<h4 id="orgd9c8dd3"><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-orga9d3ee8" class="outline-5">
<h5 id="orga9d3ee8"><span class="section-number-5">3.3.2.1</span> Function declarations</h5>
<div id="outline-container-org0bab725" class="outline-5">
<h5 id="org0bab725"><span class="section-number-5">3.3.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-orgae612b7" class="outline-5">
<h5 id="orgae612b7"><span class="section-number-5">3.3.2.2</span> Source code for double precision functions</h5>
<div id="outline-container-orgf30a05f" class="outline-5">
<h5 id="orgf30a05f"><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-orgacfd7ae" class="outline-5">
<h5 id="orgacfd7ae"><span class="section-number-5">3.3.2.3</span> Source code for single precision functions</h5>
<div id="outline-container-org76bbfe0" class="outline-5">
<h5 id="org76bbfe0"><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-org06879f2" class="outline-5">
<h5 id="org06879f2"><span class="section-number-5">3.3.2.4</span> Source code for memory-safe functions</h5>
<div id="outline-container-org76c152b" class="outline-5">
<h5 id="org76c152b"><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="orge77a79f"><span style="color: #228b22;">trexio_exit_code</span> <span style="color: #a0522d;">rc</span>;
<pre class="src src-c" id="org75307eb"><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-org32c325e" class="outline-5">
<h5 id="org32c325e"><span class="section-number-5">3.3.2.5</span> Source code for default functions</h5>
<div id="outline-container-org7678f8f" class="outline-5">
<h5 id="org7678f8f"><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-org868cea9" class="outline-4">
<h4 id="org868cea9"><span class="section-number-4">3.3.3</span> Fortran templates for front end</h4>
<div id="outline-container-org37bd15c" class="outline-4">
<h4 id="org37bd15c"><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-org086e334" class="outline-4">
<h4 id="org086e334"><span class="section-number-4">3.3.4</span> Python templates for front end</h4>
<div id="outline-container-org3a86462" class="outline-4">
<h4 id="org3a86462"><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-org7bffb82" class="outline-3">
<h3 id="org7bffb82"><span class="section-number-3">3.4</span> Sparse data structures</h3>
<div id="outline-container-orge763eef" class="outline-3">
<h3 id="orge763eef"><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-orga10aa96" class="outline-3">
<h3 id="orga10aa96"><span class="section-number-3">3.5</span> Templates for front end has/read/write a dataset of strings</h3>
<div id="outline-container-org41df8f6" class="outline-3">
<h3 id="org41df8f6"><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-org53d449d" class="outline-4">
<h4 id="org53d449d"><span class="section-number-4">3.5.1</span> Introduction</h4>
<div id="outline-container-org2d52fef" class="outline-4">
<h4 id="org2d52fef"><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-orgc24c4c7" class="outline-4">
<h4 id="orgc24c4c7"><span class="section-number-4">3.5.2</span> C templates for front end</h4>
<div id="outline-container-org63d2cab" class="outline-4">
<h4 id="org63d2cab"><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-org56f44a8" class="outline-5">
<h5 id="org56f44a8"><span class="section-number-5">3.5.2.1</span> Function declarations</h5>
<div id="outline-container-orgaf1e835" class="outline-5">
<h5 id="orgaf1e835"><span class="section-number-5">3.5.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-org1dc15fe" class="outline-5">
<h5 id="org1dc15fe"><span class="section-number-5">3.5.2.2</span> Source code for default functions</h5>
<div id="outline-container-orgeff74dc" class="outline-5">
<h5 id="orgeff74dc"><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-org6c39cea" class="outline-4">
<h4 id="org6c39cea"><span class="section-number-4">3.5.3</span> Fortran templates for front end</h4>
<div id="outline-container-org4573f63" class="outline-4">
<h4 id="org4573f63"><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-org9e1fd4a" class="outline-4">
<h4 id="org9e1fd4a"><span class="section-number-4">3.5.4</span> Python templates for front end</h4>
<div id="outline-container-orgcdfb9e8" class="outline-4">
<h4 id="orgcdfb9e8"><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-org2465a60" class="outline-3">
<h3 id="org2465a60"><span class="section-number-3">3.6</span> Templates for front end has/read/write a single string attribute</h3>
<div id="outline-container-orgbb8712c" class="outline-3">
<h3 id="orgbb8712c"><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-org941f7fe" class="outline-4">
<h4 id="org941f7fe"><span class="section-number-4">3.6.1</span> Introduction</h4>
<div id="outline-container-orga1f906e" class="outline-4">
<h4 id="orga1f906e"><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-orga68b075" class="outline-4">
<h4 id="orga68b075"><span class="section-number-4">3.6.2</span> C templates for front end</h4>
<div id="outline-container-orge414cdd" class="outline-4">
<h4 id="orge414cdd"><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-org4950592" class="outline-5">
<h5 id="org4950592"><span class="section-number-5">3.6.2.1</span> Function declarations</h5>
<div id="outline-container-org7275750" class="outline-5">
<h5 id="org7275750"><span class="section-number-5">3.6.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-orgf608d87" class="outline-5">
<h5 id="orgf608d87"><span class="section-number-5">3.6.2.2</span> Source code for default functions</h5>
<div id="outline-container-org74f3fd4" class="outline-5">
<h5 id="org74f3fd4"><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-orgd6b81f1" class="outline-4">
<h4 id="orgd6b81f1"><span class="section-number-4">3.6.3</span> Fortran templates for front end</h4>
<div id="outline-container-org3348112" class="outline-4">
<h4 id="org3348112"><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-org18811a1" class="outline-4">
<h4 id="org18811a1"><span class="section-number-4">3.6.4</span> Python templates for front end</h4>
<div id="outline-container-orge8583f1" class="outline-4">
<h4 id="orge8583f1"><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-orgff37ee5" class="outline-2">
<h2 id="orgff37ee5"><span class="section-number-2">4</span> Fortran helper/wrapper functions</h2>
<div id="outline-container-org994aafe" class="outline-2">
<h2 id="org994aafe"><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: 2021-11-17 Wed 13:18</p>
<p class="date">Created: 2021-11-17 Wed 13:23</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>
<!-- 2021-11-17 Wed 13:18 -->
<!-- 2021-11-17 Wed 13:23 -->
<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="#org12bffd5">1. HDF5 back end</a>
<li><a href="#org09bcc65">1. HDF5 back end</a>
<ul>
<li><a href="#orgc27b3ca">1.1. Template for HDF5 definitions</a></li>
<li><a href="#org0cc2ce1">1.2. Template for HDF5 structures</a></li>
<li><a href="#orgf324fea">1.3. Template for HDF5 init/deinit</a></li>
<li><a href="#org575253d">1.4. Template for HDF5 has/read/write the numerical attribute</a></li>
<li><a href="#orgf898180">1.5. Template for HDF5 has/read/write the dataset of numerical data</a></li>
<li><a href="#orgd93fac0">1.6. Template for HDF5 has/read/write the dataset of strings</a></li>
<li><a href="#orgf7177cd">1.7. Template for HDF5 has/read/write the string attribute</a></li>
<li><a href="#org481c294">1.1. Template for HDF5 definitions</a></li>
<li><a href="#org82f3d82">1.2. Template for HDF5 structures</a></li>
<li><a href="#org776392b">1.3. Template for HDF5 init/deinit</a></li>
<li><a href="#orge605500">1.4. Template for HDF5 has/read/write the numerical attribute</a></li>
<li><a href="#org6e12c35">1.5. Template for HDF5 has/read/write the dataset of numerical data</a></li>
<li><a href="#org0abcfb6">1.6. Template for HDF5 has/read/write the dataset of strings</a></li>
<li><a href="#orgeda7d19">1.7. Template for HDF5 has/read/write the string attribute</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org12bffd5" class="outline-2">
<h2 id="org12bffd5"><span class="section-number-2">1</span> HDF5 back end</h2>
<div id="outline-container-org09bcc65" class="outline-2">
<h2 id="org09bcc65"><span class="section-number-2">1</span> HDF5 back end</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-orgc27b3ca" class="outline-3">
<h3 id="orgc27b3ca"><span class="section-number-3">1.1</span> Template for HDF5 definitions</h3>
<div id="outline-container-org481c294" class="outline-3">
<h3 id="org481c294"><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-org0cc2ce1" class="outline-3">
<h3 id="org0cc2ce1"><span class="section-number-3">1.2</span> Template for HDF5 structures</h3>
<div id="outline-container-org82f3d82" class="outline-3">
<h3 id="org82f3d82"><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-orgf324fea" class="outline-3">
<h3 id="orgf324fea"><span class="section-number-3">1.3</span> Template for HDF5 init/deinit</h3>
<div id="outline-container-org776392b" class="outline-3">
<h3 id="org776392b"><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-org575253d" class="outline-3">
<h3 id="org575253d"><span class="section-number-3">1.4</span> Template for HDF5 has/read/write the numerical attribute</h3>
<div id="outline-container-orge605500" class="outline-3">
<h3 id="orge605500"><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-orgf898180" class="outline-3">
<h3 id="orgf898180"><span class="section-number-3">1.5</span> Template for HDF5 has/read/write the dataset of numerical data</h3>
<div id="outline-container-org6e12c35" class="outline-3">
<h3 id="org6e12c35"><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-orgd93fac0" class="outline-3">
<h3 id="orgd93fac0"><span class="section-number-3">1.6</span> Template for HDF5 has/read/write the dataset of strings</h3>
<div id="outline-container-org0abcfb6" class="outline-3">
<h3 id="org0abcfb6"><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-orgf7177cd" class="outline-3">
<h3 id="orgf7177cd"><span class="section-number-3">1.7</span> Template for HDF5 has/read/write the string attribute</h3>
<div id="outline-container-orgeda7d19" class="outline-3">
<h3 id="orgeda7d19"><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: 2021-11-17 Wed 13:18</p>
<p class="date">Created: 2021-11-17 Wed 13:23</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>
<!-- 2021-11-17 Wed 13:18 -->
<!-- 2021-11-17 Wed 13:23 -->
<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="#org131a8c2">1. TEXT back end</a>
<li><a href="#orgd33d4b9">1. TEXT back end</a>
<ul>
<li><a href="#org98c71c2">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#org5991264">1.2. Template for general structure in text back end</a></li>
<li><a href="#orgde1d757">1.3. Initialize function (constant part)</a></li>
<li><a href="#orgb6d43eb">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#org1d2254b">1.5. Template for text read struct</a></li>
<li><a href="#orgef535dd">1.6. Template for text flush struct</a></li>
<li><a href="#org6c7b8fd">1.7. Template for text free memory</a></li>
<li><a href="#org90e6d3c">1.8. Template for has/read/write the numerical attribute</a></li>
<li><a href="#org2b05531">1.9. Template for has/read/write the dataset of numerical data</a></li>
<li><a href="#org4eb994c">1.10. Template for has/read/write the dataset of strings</a></li>
<li><a href="#org2fc8b89">1.11. Template for has/read/write the string attribute</a></li>
<li><a href="#orga642930">1.12. RDM struct (hard-coded)</a>
<li><a href="#orga8096da">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#orga90f9cb">1.2. Template for general structure in text back end</a></li>
<li><a href="#orgee63fb2">1.3. Initialize function (constant part)</a></li>
<li><a href="#orgc651a3b">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#org07b9817">1.5. Template for text read struct</a></li>
<li><a href="#org234bb6f">1.6. Template for text flush struct</a></li>
<li><a href="#orgefbcb25">1.7. Template for text free memory</a></li>
<li><a href="#orgdf704d2">1.8. Template for has/read/write the numerical attribute</a></li>
<li><a href="#orgcb28077">1.9. Template for has/read/write the dataset of numerical data</a></li>
<li><a href="#orgeb117a1">1.10. Template for has/read/write the dataset of strings</a></li>
<li><a href="#org8d91fcc">1.11. Template for has/read/write the string attribute</a></li>
<li><a href="#org0aeef70">1.12. RDM struct (hard-coded)</a>
<ul>
<li><a href="#org681c0a5">1.12.1. Read the complete struct</a></li>
<li><a href="#org419e9ce">1.12.2. Flush the complete struct</a></li>
<li><a href="#org976a12a">1.12.3. Free memory</a></li>
<li><a href="#org7b07ae9">1.12.4. Read/Write the one<sub>e</sub> attribute</a></li>
<li><a href="#org6103c43">1.12.5. Read/Write the two<sub>e</sub> attribute</a></li>
<li><a href="#org66242b3">1.12.1. Read the complete struct</a></li>
<li><a href="#org433e91f">1.12.2. Flush the complete struct</a></li>
<li><a href="#orgd6c4aa3">1.12.3. Free memory</a></li>
<li><a href="#org8a87c09">1.12.4. Read/Write the one<sub>e</sub> attribute</a></li>
<li><a href="#orgbb28ff5">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-org131a8c2" class="outline-2">
<h2 id="org131a8c2"><span class="section-number-2">1</span> TEXT back end</h2>
<div id="outline-container-orgd33d4b9" class="outline-2">
<h2 id="orgd33d4b9"><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-org98c71c2" class="outline-3">
<h3 id="org98c71c2"><span class="section-number-3">1.1</span> Template for group-related structures in text back end</h3>
<div id="outline-container-orga8096da" class="outline-3">
<h3 id="orga8096da"><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-org5991264" class="outline-3">
<h3 id="org5991264"><span class="section-number-3">1.2</span> Template for general structure in text back end</h3>
<div id="outline-container-orga90f9cb" class="outline-3">
<h3 id="orga90f9cb"><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-orgde1d757" class="outline-3">
<h3 id="orgde1d757"><span class="section-number-3">1.3</span> Initialize function (constant part)</h3>
<div id="outline-container-orgee63fb2" class="outline-3">
<h3 id="orgee63fb2"><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-orgb6d43eb" class="outline-3">
<h3 id="orgb6d43eb"><span class="section-number-3">1.4</span> Deinitialize function (templated part)</h3>
<div id="outline-container-orgc651a3b" class="outline-3">
<h3 id="orgc651a3b"><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-org1d2254b" class="outline-3">
<h3 id="org1d2254b"><span class="section-number-3">1.5</span> Template for text read struct</h3>
<div id="outline-container-org07b9817" class="outline-3">
<h3 id="org07b9817"><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-orgef535dd" class="outline-3">
<h3 id="orgef535dd"><span class="section-number-3">1.6</span> Template for text flush struct</h3>
<div id="outline-container-org234bb6f" class="outline-3">
<h3 id="org234bb6f"><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-org6c7b8fd" class="outline-3">
<h3 id="org6c7b8fd"><span class="section-number-3">1.7</span> Template for text free memory</h3>
<div id="outline-container-orgefbcb25" class="outline-3">
<h3 id="orgefbcb25"><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-org90e6d3c" class="outline-3">
<h3 id="org90e6d3c"><span class="section-number-3">1.8</span> Template for has/read/write the numerical attribute</h3>
<div id="outline-container-orgdf704d2" class="outline-3">
<h3 id="orgdf704d2"><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-org2b05531" class="outline-3">
<h3 id="org2b05531"><span class="section-number-3">1.9</span> Template for has/read/write the dataset of numerical data</h3>
<div id="outline-container-orgcb28077" class="outline-3">
<h3 id="orgcb28077"><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-org4eb994c" class="outline-3">
<h3 id="org4eb994c"><span class="section-number-3">1.10</span> Template for has/read/write the dataset of strings</h3>
<div id="outline-container-orgeb117a1" class="outline-3">
<h3 id="orgeb117a1"><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-org2fc8b89" class="outline-3">
<h3 id="org2fc8b89"><span class="section-number-3">1.11</span> Template for has/read/write the string attribute</h3>
<div id="outline-container-org8d91fcc" class="outline-3">
<h3 id="org8d91fcc"><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-orga642930" class="outline-3">
<h3 id="orga642930"><span class="section-number-3">1.12</span> RDM struct (hard-coded)</h3>
<div id="outline-container-org0aeef70" class="outline-3">
<h3 id="org0aeef70"><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-org681c0a5" class="outline-4">
<h4 id="org681c0a5"><span class="section-number-4">1.12.1</span> Read the complete struct</h4>
<div id="outline-container-org66242b3" class="outline-4">
<h4 id="org66242b3"><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-org419e9ce" class="outline-4">
<h4 id="org419e9ce"><span class="section-number-4">1.12.2</span> Flush the complete struct</h4>
<div id="outline-container-org433e91f" class="outline-4">
<h4 id="org433e91f"><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-org976a12a" class="outline-4">
<h4 id="org976a12a"><span class="section-number-4">1.12.3</span> Free memory</h4>
<div id="outline-container-orgd6c4aa3" class="outline-4">
<h4 id="orgd6c4aa3"><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-org7b07ae9" class="outline-4">
<h4 id="org7b07ae9"><span class="section-number-4">1.12.4</span> Read/Write the one<sub>e</sub> attribute</h4>
<div id="outline-container-org8a87c09" class="outline-4">
<h4 id="org8a87c09"><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-org6103c43" class="outline-4">
<h4 id="org6103c43"><span class="section-number-4">1.12.5</span> Read/Write the two<sub>e</sub> attribute</h4>
<div id="outline-container-orgbb28ff5" class="outline-4">
<h4 id="orgbb28ff5"><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: 2021-11-17 Wed 13:18</p>
<p class="date">Created: 2021-11-17 Wed 13:23</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

116
trex.html
View File

@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2021-11-17 Wed 13:18 -->
<!-- 2021-11-17 Wed 13:23 -->
<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="#org5d35540">1. Metadata (metadata group)</a></li>
<li><a href="#org6630ad3">2. Electron (electron group)</a></li>
<li><a href="#orgca40772">3. Nucleus (nucleus group)</a></li>
<li><a href="#orga4319c6">4. Effective core potentials (ecp group)</a>
<li><a href="#org08b10a1">1. Metadata (metadata group)</a></li>
<li><a href="#org1af947a">2. Electron (electron group)</a></li>
<li><a href="#org5075112">3. Nucleus (nucleus group)</a></li>
<li><a href="#orga1079c0">4. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org0768341">4.1. Example</a></li>
<li><a href="#org373a100">4.1. Example</a></li>
</ul>
</li>
<li><a href="#org9d02681">5. Basis set (basis group)</a>
<li><a href="#orga70d288">5. Basis set (basis group)</a>
<ul>
<li><a href="#org97facfc">5.1. Example</a></li>
<li><a href="#org0334663">5.1. Example</a></li>
</ul>
</li>
<li><a href="#org0144202">6. Atomic orbitals (ao group)</a>
<li><a href="#org84800d2">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="#org710ba6a">7. Molecular orbitals (mo group)</a>
<li><a href="#org633bc24">7. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#orgc7f08ea">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgee4424e">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org297b409">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgf1768cf">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#orgc2af6e9">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#org9bdaed1">9. <span class="todo TODO">TODO</span> Reduced density matrices (rdm group)</a></li>
<li><a href="#orgdd0c0bb">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#org396b22a">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-org5d35540" class="outline-2">
<h2 id="org5d35540"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org08b10a1" class="outline-2">
<h2 id="org08b10a1"><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="org061ac1e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org533a244" 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-org6630ad3" class="outline-2">
<h2 id="org6630ad3"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div id="outline-container-org1af947a" class="outline-2">
<h2 id="org1af947a"><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="org2c62bf1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgcf2f6c9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -524,15 +524,15 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-orgca40772" class="outline-2">
<h2 id="orgca40772"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div id="outline-container-org5075112" class="outline-2">
<h2 id="org5075112"><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="orga24f0b4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org159e63d" 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-orga4319c6" class="outline-2">
<h2 id="orga4319c6"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div id="outline-container-orga1079c0" class="outline-2">
<h2 id="orga1079c0"><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="org5846300" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org0334a70" 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-org0768341" class="outline-3">
<h3 id="org0768341"><span class="section-number-3">4.1</span> Example</h3>
<div id="outline-container-org373a100" class="outline-3">
<h3 id="org373a100"><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-org9d02681" class="outline-2">
<h2 id="org9d02681"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div id="outline-container-orga70d288" class="outline-2">
<h2 id="orga70d288"><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="org1afffa2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgfe5143f" 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-org97facfc" class="outline-3">
<h3 id="org97facfc"><span class="section-number-3">5.1</span> Example</h3>
<div id="outline-container-org0334663" class="outline-3">
<h3 id="org0334663"><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-org0144202" class="outline-2">
<h2 id="org0144202"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div id="outline-container-org84800d2" class="outline-2">
<h2 id="org84800d2"><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="#org9d02681">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#orga70d288">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="orgca797da" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgbb99340" 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-org45f47d0" class="outline-3">
<h3 id="ao_one_e"><a id="org45f47d0"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div id="outline-container-org4492a48" class="outline-3">
<h3 id="ao_one_e"><a id="org4492a48"></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="org514215d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5e0c567" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1208,8 +1208,8 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org70171cf" class="outline-3">
<h3 id="ao_two_e"><a id="org70171cf"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div id="outline-container-org06296f8" class="outline-3">
<h3 id="ao_two_e"><a id="org06296f8"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div class="outline-text-3" id="text-ao_two_e">
<p>
The two-electron integrals for a two-electron operator \(\hat{O}\) are
@ -1230,7 +1230,7 @@ notation.
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
</ul>
<table id="orge04b124" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org49d54f7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1270,10 +1270,10 @@ notation.
</div>
</div>
<div id="outline-container-org710ba6a" class="outline-2">
<h2 id="org710ba6a"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div id="outline-container-org633bc24" class="outline-2">
<h2 id="org633bc24"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div class="outline-text-2" id="text-7">
<table id="org950c653" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
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@ -1339,8 +1339,8 @@ notation.
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<h3 id="orgc7f08ea"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
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<h3 id="org297b409"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
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<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.
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@ -1415,8 +1415,8 @@ the basis of molecular orbitals.
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<h3 id="orgee4424e"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
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<h3 id="orgf1768cf"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
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<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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@ -1464,13 +1464,13 @@ the basis of molecular orbitals.
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<h2 id="orgc2af6e9"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
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<h2 id="orgdd0c0bb"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
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<h2 id="org9bdaed1"><span class="section-number-2">9</span> <span class="todo TODO">TODO</span> Reduced density matrices (rdm group)</h2>
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<h2 id="org396b22a"><span class="section-number-2">9</span> <span class="todo TODO">TODO</span> Reduced density matrices (rdm group)</h2>
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@ -1525,7 +1525,7 @@ the basis of molecular orbitals.
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<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2021-11-17 Wed 13:18</p>
<p class="date">Created: 2021-11-17 Wed 13:23</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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