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4
README.html
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head> <head>
<!-- 2021-06-22 Tue 09:38 --> <!-- 2021-06-22 Tue 10:22 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" /> <meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" /> <meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title> <title>TREXIO source code documentation</title>
@ -342,7 +342,7 @@ and bug reports should be submitted at
</div> </div>
<div id="postamble" class="status"> <div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p> <p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2021-06-22 Tue 09:38</p> <p class="date">Created: 2021-06-22 Tue 10:22</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p> <p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div> </div>
</body> </body>

16
Sparse.html
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head> <head>
<!-- 2021-06-22 Tue 09:38 --> <!-- 2021-06-22 Tue 10:22 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" /> <meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" /> <meta name="viewport" content="width=device-width, initial-scale=1" />
<title>&lrm;</title> <title>&lrm;</title>
@ -232,8 +232,8 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2> <h2>Table of Contents</h2>
<div id="text-table-of-contents"> <div id="text-table-of-contents">
<ul> <ul>
<li><a href="#orga8aeee4">1. Text back end</a></li> <li><a href="#org72f5cf5">1. Text back end</a></li>
<li><a href="#org4d817d2">2. HDF5 Back end</a></li> <li><a href="#org055c88d">2. HDF5 Back end</a></li>
</ul> </ul>
</div> </div>
</div> </div>
@ -241,8 +241,8 @@ for the JavaScript code in this tag.
See templator<sub>front.org</sub> See templator<sub>front.org</sub>
</p> </p>
<div id="outline-container-orga8aeee4" class="outline-2"> <div id="outline-container-org72f5cf5" class="outline-2">
<h2 id="orga8aeee4"><span class="section-number-2">1</span> Text back end</h2> <h2 id="org72f5cf5"><span class="section-number-2">1</span> Text back end</h2>
<div class="outline-text-2" id="text-1"> <div class="outline-text-2" id="text-1">
<p> <p>
As the size of the dataset should be extensible, the simplest 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> </div>
<div id="outline-container-org4d817d2" class="outline-2"> <div id="outline-container-org055c88d" class="outline-2">
<h2 id="org4d817d2"><span class="section-number-2">2</span> HDF5 Back end</h2> <h2 id="org055c88d"><span class="section-number-2">2</span> HDF5 Back end</h2>
<div class="outline-text-2" id="text-2"> <div class="outline-text-2" id="text-2">
<p> <p>
We need to declare the number of rows of the dataset as 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> </div>
<div id="postamble" class="status"> <div id="postamble" class="status">
<p class="date">Created: 2021-06-22 Tue 09:38</p> <p class="date">Created: 2021-06-22 Tue 10:22</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p> <p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div> </div>
</body> </body>

4
index.html
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head> <head>
<!-- 2021-06-22 Tue 09:38 --> <!-- 2021-06-22 Tue 10:22 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" /> <meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" /> <meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title> <title>TREXIO source code documentation</title>
@ -342,7 +342,7 @@ and bug reports should be submitted at
</div> </div>
<div id="postamble" class="status"> <div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p> <p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2021-06-22 Tue 09:38</p> <p class="date">Created: 2021-06-22 Tue 10:22</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p> <p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div> </div>
</body> </body>

174
templator_front.html
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head> <head>
<!-- 2021-06-22 Tue 09:38 --> <!-- 2021-06-22 Tue 10:22 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" /> <meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" /> <meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Front end API</title> <title>Front end API</title>
@ -333,61 +333,61 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2> <h2>Table of Contents</h2>
<div id="text-table-of-contents"> <div id="text-table-of-contents">
<ul> <ul>
<li><a href="#org6f6e16c">1. Coding conventions</a> <li><a href="#org825a5a0">1. Coding conventions</a>
<ul> <ul>
<li><a href="#orgd33db8b">1.1. Memory allocation</a></li> <li><a href="#orge2f8a55">1.1. Memory allocation</a></li>
</ul> </ul>
</li> </li>
<li><a href="#org11d4421">2. Front end</a> <li><a href="#org96fc97d">2. Front end</a>
<ul> <ul>
<li><a href="#org8295bcd">2.1. Error handling</a></li> <li><a href="#orgc0d8632">2.1. Error handling</a></li>
<li><a href="#orgf39acfc">2.2. Back ends</a></li> <li><a href="#org0aa5079">2.2. Back ends</a></li>
<li><a href="#orgf38bf62">2.3. Read/write behavior</a></li> <li><a href="#org8c7226e">2.3. Read/write behavior</a></li>
<li><a href="#orgde502de">2.4. TREXIO file type</a></li> <li><a href="#orga195db7">2.4. TREXIO file type</a></li>
<li><a href="#orga4fcaad">2.5. Polymorphism of the file handle</a></li> <li><a href="#orgf2c3ab7">2.5. Polymorphism of the file handle</a></li>
<li><a href="#org07f58bb">2.6. File opening</a></li> <li><a href="#org73bd8f3">2.6. File opening</a></li>
<li><a href="#org530176e">2.7. File closing</a></li> <li><a href="#orgd6e06c9">2.7. File closing</a></li>
</ul> </ul>
</li> </li>
<li><a href="#org025d7a9">3. Templates for front end</a> <li><a href="#orgdf1e9c4">3. Templates for front end</a>
<ul> <ul>
<li><a href="#orgfb6c9d3">3.1. Description</a></li> <li><a href="#orgaec4c11">3.1. Description</a></li>
<li><a href="#orgbb47b5c">3.2. Templates for front end has/read/write a single dimensioning variable</a> <li><a href="#orgdb20b39">3.2. Templates for front end has/read/write a single dimensioning variable</a>
<ul> <ul>
<li><a href="#org53efe5d">3.2.1. C templates for front end</a></li> <li><a href="#orgb169558">3.2.1. C templates for front end</a></li>
<li><a href="#org3d82b05">3.2.2. Fortran templates for front end</a></li> <li><a href="#org5e69b90">3.2.2. Fortran templates for front end</a></li>
</ul> </ul>
</li> </li>
<li><a href="#orga900ee7">3.3. Templates for front end has/read/write a dataset of numerical data</a> <li><a href="#org5d80755">3.3. Templates for front end has/read/write a dataset of numerical data</a>
<ul> <ul>
<li><a href="#org7b7e6ce">3.3.1. C templates for front end</a></li> <li><a href="#org16585b5">3.3.1. C templates for front end</a></li>
<li><a href="#orgd35a49f">3.3.2. Fortran templates for front end</a></li> <li><a href="#orge4a641e">3.3.2. Fortran templates for front end</a></li>
</ul> </ul>
</li> </li>
<li><a href="#orgda05337">3.4. Sparse data structures</a></li> <li><a href="#orgf888836">3.4. Sparse data structures</a></li>
<li><a href="#org9afb2f0">3.5. Templates for front end has/read/write a dataset of strings</a> <li><a href="#org93f30b9">3.5. Templates for front end has/read/write a dataset of strings</a>
<ul> <ul>
<li><a href="#org5709d3b">3.5.1. Introduction</a></li> <li><a href="#orgba96594">3.5.1. Introduction</a></li>
<li><a href="#orgf7f8949">3.5.2. C templates for front end</a></li> <li><a href="#orgfa762ea">3.5.2. C templates for front end</a></li>
<li><a href="#org1c5e24d">3.5.3. Fortran templates for front end</a></li> <li><a href="#org2346c52">3.5.3. Fortran templates for front end</a></li>
</ul> </ul>
</li> </li>
<li><a href="#orgc08fae5">3.6. Templates for front end has/read/write a single string attribute</a> <li><a href="#orgb7b49c5">3.6. Templates for front end has/read/write a single string attribute</a>
<ul> <ul>
<li><a href="#org9aa4dea">3.6.1. Introduction</a></li> <li><a href="#org98b2793">3.6.1. Introduction</a></li>
<li><a href="#org6edcce1">3.6.2. C templates for front end</a></li> <li><a href="#orgab59381">3.6.2. C templates for front end</a></li>
<li><a href="#org4e5b793">3.6.3. Fortran templates for front end</a></li> <li><a href="#orgf778bf1">3.6.3. Fortran templates for front end</a></li>
</ul> </ul>
</li> </li>
</ul> </ul>
</li> </li>
<li><a href="#org2ed9d42">4. Fortran helper/wrapper functions</a></li> <li><a href="#orge3060b4">4. Fortran helper/wrapper functions</a></li>
</ul> </ul>
</div> </div>
</div> </div>
<div id="outline-container-org6f6e16c" class="outline-2"> <div id="outline-container-org825a5a0" class="outline-2">
<h2 id="org6f6e16c"><span class="section-number-2">1</span> Coding conventions</h2> <h2 id="org825a5a0"><span class="section-number-2">1</span> Coding conventions</h2>
<div class="outline-text-2" id="text-1"> <div class="outline-text-2" id="text-1">
<ul class="org-ul"> <ul class="org-ul">
<li>integer types will be defined using types given in <code>stdint.h</code></li> <li>integer types will be defined using types given in <code>stdint.h</code></li>
@ -402,8 +402,8 @@ for the JavaScript code in this tag.
</ul> </ul>
</div> </div>
<div id="outline-container-orgd33db8b" class="outline-3"> <div id="outline-container-orge2f8a55" class="outline-3">
<h3 id="orgd33db8b"><span class="section-number-3">1.1</span> Memory allocation</h3> <h3 id="orge2f8a55"><span class="section-number-3">1.1</span> Memory allocation</h3>
<div class="outline-text-3" id="text-1-1"> <div class="outline-text-3" id="text-1-1">
<p> <p>
Memory allocation of structures can be facilitated by using the Memory allocation of structures can be facilitated by using the
@ -438,8 +438,8 @@ The maximum string size for the filenames is 4096 characters.
</div> </div>
</div> </div>
<div id="outline-container-org11d4421" class="outline-2"> <div id="outline-container-org96fc97d" class="outline-2">
<h2 id="org11d4421"><span class="section-number-2">2</span> Front end</h2> <h2 id="org96fc97d"><span class="section-number-2">2</span> Front end</h2>
<div class="outline-text-2" id="text-2"> <div class="outline-text-2" id="text-2">
<p> <p>
All calls to TREXIO are thread-safe. All calls to TREXIO are thread-safe.
@ -447,10 +447,10 @@ TREXIO front end is modular, which simplifies implementation of new back ends.
</p> </p>
</div> </div>
<div id="outline-container-org8295bcd" class="outline-3"> <div id="outline-container-orgc0d8632" class="outline-3">
<h3 id="org8295bcd"><span class="section-number-3">2.1</span> Error handling</h3> <h3 id="orgc0d8632"><span class="section-number-3">2.1</span> Error handling</h3>
<div class="outline-text-3" id="text-2-1"> <div class="outline-text-3" id="text-2-1">
<table id="orgdf3bb3f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides"> <table id="org1997f08" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup> <colgroup>
@ -750,8 +750,8 @@ The text strings are extracted from the previous table.
</div> </div>
</div> </div>
<div id="outline-container-orgf39acfc" class="outline-3"> <div id="outline-container-org0aa5079" class="outline-3">
<h3 id="orgf39acfc"><span class="section-number-3">2.2</span> Back ends</h3> <h3 id="org0aa5079"><span class="section-number-3">2.2</span> Back ends</h3>
<div class="outline-text-3" id="text-2-2"> <div class="outline-text-3" id="text-2-2">
<p> <p>
TREXIO has several back ends: TREXIO has several back ends:
@ -783,8 +783,8 @@ lines that correspond to the <code>TREXIO_JSON</code> back end (not implemented
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-orgf38bf62" class="outline-3"> <div id="outline-container-org8c7226e" class="outline-3">
<h3 id="orgf38bf62"><span class="section-number-3">2.3</span> Read/write behavior</h3> <h3 id="org8c7226e"><span class="section-number-3">2.3</span> Read/write behavior</h3>
<div class="outline-text-3" id="text-2-3"> <div class="outline-text-3" id="text-2-3">
<p> <p>
Every time a reading function is called, the data is read from the Every time a reading function is called, the data is read from the
@ -812,8 +812,8 @@ concurrent programs, the behavior is not specified.
</p> </p>
</div> </div>
</div> </div>
<div id="outline-container-orgde502de" class="outline-3"> <div id="outline-container-orga195db7" class="outline-3">
<h3 id="orgde502de"><span class="section-number-3">2.4</span> TREXIO file type</h3> <h3 id="orga195db7"><span class="section-number-3">2.4</span> TREXIO file type</h3>
<div class="outline-text-3" id="text-2-4"> <div class="outline-text-3" id="text-2-4">
<p> <p>
<code>trexio_s</code> is the the main type for TREXIO files, visible to the users <code>trexio_s</code> is the the main type for TREXIO files, visible to the users
@ -846,8 +846,8 @@ TREXIO files will have as a first argument the TREXIO file handle.
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-orga4fcaad" class="outline-3"> <div id="outline-container-orgf2c3ab7" class="outline-3">
<h3 id="orga4fcaad"><span class="section-number-3">2.5</span> Polymorphism of the file handle</h3> <h3 id="orgf2c3ab7"><span class="section-number-3">2.5</span> Polymorphism of the file handle</h3>
<div class="outline-text-3" id="text-2-5"> <div class="outline-text-3" id="text-2-5">
<p> <p>
Polymorphism of the <code>trexio_t</code> type is handled by ensuring that the Polymorphism of the <code>trexio_t</code> type is handled by ensuring that the
@ -866,8 +866,8 @@ corresponding types for all back ends can be safely casted to
</div> </div>
</div> </div>
<div id="outline-container-org07f58bb" class="outline-3"> <div id="outline-container-org73bd8f3" class="outline-3">
<h3 id="org07f58bb"><span class="section-number-3">2.6</span> File opening</h3> <h3 id="org73bd8f3"><span class="section-number-3">2.6</span> File opening</h3>
<div class="outline-text-3" id="text-2-6"> <div class="outline-text-3" id="text-2-6">
<p> <p>
<code>trexio_open</code> creates a new TREXIO file or opens existing one. <code>trexio_open</code> creates a new TREXIO file or opens existing one.
@ -1058,8 +1058,8 @@ know if we need to shift by 1 arrays of indices.
</div> </div>
</div> </div>
<div id="outline-container-org530176e" class="outline-3"> <div id="outline-container-orgd6e06c9" class="outline-3">
<h3 id="org530176e"><span class="section-number-3">2.7</span> File closing</h3> <h3 id="orgd6e06c9"><span class="section-number-3">2.7</span> File closing</h3>
<div class="outline-text-3" id="text-2-7"> <div class="outline-text-3" id="text-2-7">
<p> <p>
<code>trexio_close</code> closes an existing <code>trexio_t</code> file. <code>trexio_close</code> closes an existing <code>trexio_t</code> file.
@ -1155,12 +1155,12 @@ output:
</div> </div>
</div> </div>
<div id="outline-container-org025d7a9" class="outline-2"> <div id="outline-container-orgdf1e9c4" class="outline-2">
<h2 id="org025d7a9"><span class="section-number-2">3</span> Templates for front end</h2> <h2 id="orgdf1e9c4"><span class="section-number-2">3</span> Templates for front end</h2>
<div class="outline-text-2" id="text-3"> <div class="outline-text-2" id="text-3">
</div> </div>
<div id="outline-container-orgfb6c9d3" class="outline-3"> <div id="outline-container-orgaec4c11" class="outline-3">
<h3 id="orgfb6c9d3"><span class="section-number-3">3.1</span> Description</h3> <h3 id="orgaec4c11"><span class="section-number-3">3.1</span> Description</h3>
<div class="outline-text-3" id="text-3-1"> <div class="outline-text-3" id="text-3-1">
<p> <p>
Consider the following block of <code>trex.json</code>: Consider the following block of <code>trex.json</code>:
@ -1350,8 +1350,8 @@ or double precision for integer and floating point numbers.
</div> </div>
</div> </div>
<div id="outline-container-orgbb47b5c" class="outline-3"> <div id="outline-container-orgdb20b39" class="outline-3">
<h3 id="orgbb47b5c"><span class="section-number-3">3.2</span> Templates for front end has/read/write a single dimensioning variable</h3> <h3 id="orgdb20b39"><span class="section-number-3">3.2</span> Templates for front end has/read/write a single dimensioning variable</h3>
<div class="outline-text-3" id="text-3-2"> <div class="outline-text-3" id="text-3-2">
<p> <p>
This section concerns API calls related to dimensioning variables. This section concerns API calls related to dimensioning variables.
@ -1420,8 +1420,8 @@ This section concerns API calls related to dimensioning variables.
</table> </table>
</div> </div>
<div id="outline-container-org53efe5d" class="outline-4"> <div id="outline-container-orgb169558" class="outline-4">
<h4 id="org53efe5d"><span class="section-number-4">3.2.1</span> C templates for front end</h4> <h4 id="orgb169558"><span class="section-number-4">3.2.1</span> C templates for front end</h4>
<div class="outline-text-4" id="text-3-2-1"> <div class="outline-text-4" id="text-3-2-1">
<p> <p>
The <code>C</code> templates that correspond to each of the abovementioned The <code>C</code> templates that correspond to each of the abovementioned
@ -1610,8 +1610,8 @@ precision (see Table above).
</div> </div>
</div> </div>
<div id="outline-container-org3d82b05" class="outline-4"> <div id="outline-container-org5e69b90" class="outline-4">
<h4 id="org3d82b05"><span class="section-number-4">3.2.2</span> Fortran templates for front end</h4> <h4 id="org5e69b90"><span class="section-number-4">3.2.2</span> Fortran templates for front end</h4>
<div class="outline-text-4" id="text-3-2-2"> <div class="outline-text-4" id="text-3-2-2">
<p> <p>
The <code>Fortran</code> templates that provide an access to the <code>C</code> API calls from Fortran. The <code>Fortran</code> templates that provide an access to the <code>C</code> API calls from Fortran.
@ -1697,8 +1697,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div> </div>
</div> </div>
<div id="outline-container-orga900ee7" class="outline-3"> <div id="outline-container-org5d80755" class="outline-3">
<h3 id="orga900ee7"><span class="section-number-3">3.3</span> Templates for front end has/read/write a dataset of numerical data</h3> <h3 id="org5d80755"><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 class="outline-text-3" id="text-3-3">
<p> <p>
This section concerns API calls related to datasets. This section concerns API calls related to datasets.
@ -1767,8 +1767,8 @@ This section concerns API calls related to datasets.
</table> </table>
</div> </div>
<div id="outline-container-org7b7e6ce" class="outline-4"> <div id="outline-container-org16585b5" class="outline-4">
<h4 id="org7b7e6ce"><span class="section-number-4">3.3.1</span> C templates for front end</h4> <h4 id="org16585b5"><span class="section-number-4">3.3.1</span> C templates for front end</h4>
<div class="outline-text-4" id="text-3-3-1"> <div class="outline-text-4" id="text-3-3-1">
<p> <p>
The C templates that correspond to each of the abovementioned functions can be found below. The C templates that correspond to each of the abovementioned functions can be found below.
@ -2087,8 +2087,8 @@ The basic (non-suffixed) API call on datasets deals with double precision (see T
</div> </div>
</div> </div>
<div id="outline-container-orgd35a49f" class="outline-4"> <div id="outline-container-orge4a641e" class="outline-4">
<h4 id="orgd35a49f"><span class="section-number-4">3.3.2</span> Fortran templates for front end</h4> <h4 id="orge4a641e"><span class="section-number-4">3.3.2</span> Fortran templates for front end</h4>
<div class="outline-text-4" id="text-3-3-2"> <div class="outline-text-4" id="text-3-3-2">
<p> <p>
The <code>Fortran</code> templates that provide an access to the <code>C</code> API calls from <code>Fortran</code>. The <code>Fortran</code> templates that provide an access to the <code>C</code> API calls from <code>Fortran</code>.
@ -2174,8 +2174,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div> </div>
</div> </div>
<div id="outline-container-orgda05337" class="outline-3"> <div id="outline-container-orgf888836" class="outline-3">
<h3 id="orgda05337"><span class="section-number-3">3.4</span> Sparse data structures</h3> <h3 id="orgf888836"><span class="section-number-3">3.4</span> Sparse data structures</h3>
<div class="outline-text-3" id="text-3-4"> <div class="outline-text-3" id="text-3-4">
<p> <p>
Sparse data structures are used typically for large tensors such as Sparse data structures are used typically for large tensors such as
@ -2316,12 +2316,12 @@ For the values,
</div> </div>
</div> </div>
<div id="outline-container-org9afb2f0" class="outline-3"> <div id="outline-container-org93f30b9" class="outline-3">
<h3 id="org9afb2f0"><span class="section-number-3">3.5</span> Templates for front end has/read/write a dataset of strings</h3> <h3 id="org93f30b9"><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 class="outline-text-3" id="text-3-5">
</div> </div>
<div id="outline-container-org5709d3b" class="outline-4"> <div id="outline-container-orgba96594" class="outline-4">
<h4 id="org5709d3b"><span class="section-number-4">3.5.1</span> Introduction</h4> <h4 id="orgba96594"><span class="section-number-4">3.5.1</span> Introduction</h4>
<div class="outline-text-4" id="text-3-5-1"> <div class="outline-text-4" id="text-3-5-1">
<p> <p>
This section concerns API calls related to datasets of strings. This section concerns API calls related to datasets of strings.
@ -2361,8 +2361,8 @@ This section concerns API calls related to datasets of strings.
</div> </div>
</div> </div>
<div id="outline-container-orgf7f8949" class="outline-4"> <div id="outline-container-orgfa762ea" class="outline-4">
<h4 id="orgf7f8949"><span class="section-number-4">3.5.2</span> C templates for front end</h4> <h4 id="orgfa762ea"><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"> <div class="outline-text-4" id="text-3-5-2">
<p> <p>
First parameter is the <code>TREXIO</code> file handle. Second parameter is the variable to be written/read First parameter is the <code>TREXIO</code> file handle. Second parameter is the variable to be written/read
@ -2605,8 +2605,8 @@ to/from the <code>TREXIO</code> file (except for <code>trexio_has_</code> functi
</div> </div>
</div> </div>
<div id="outline-container-org1c5e24d" class="outline-4"> <div id="outline-container-org2346c52" class="outline-4">
<h4 id="org1c5e24d"><span class="section-number-4">3.5.3</span> Fortran templates for front end</h4> <h4 id="org2346c52"><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"> <div class="outline-text-4" id="text-3-5-3">
<p> <p>
The <code>Fortran</code> templates that provide an access to the <code>C</code> API calls from <code>Fortran</code>. The <code>Fortran</code> templates that provide an access to the <code>C</code> API calls from <code>Fortran</code>.
@ -2703,12 +2703,12 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div> </div>
</div> </div>
<div id="outline-container-orgc08fae5" class="outline-3"> <div id="outline-container-orgb7b49c5" class="outline-3">
<h3 id="orgc08fae5"><span class="section-number-3">3.6</span> Templates for front end has/read/write a single string attribute</h3> <h3 id="orgb7b49c5"><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 class="outline-text-3" id="text-3-6">
</div> </div>
<div id="outline-container-org9aa4dea" class="outline-4"> <div id="outline-container-org98b2793" class="outline-4">
<h4 id="org9aa4dea"><span class="section-number-4">3.6.1</span> Introduction</h4> <h4 id="org98b2793"><span class="section-number-4">3.6.1</span> Introduction</h4>
<div class="outline-text-4" id="text-3-6-1"> <div class="outline-text-4" id="text-3-6-1">
<p> <p>
This section concerns API calls related to string attributes. This section concerns API calls related to string attributes.
@ -2748,8 +2748,8 @@ This section concerns API calls related to string attributes.
</div> </div>
</div> </div>
<div id="outline-container-org6edcce1" class="outline-4"> <div id="outline-container-orgab59381" class="outline-4">
<h4 id="org6edcce1"><span class="section-number-4">3.6.2</span> C templates for front end</h4> <h4 id="orgab59381"><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 class="outline-text-4" id="text-3-6-2">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span> <pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -2849,8 +2849,8 @@ This section concerns API calls related to string attributes.
</div> </div>
</div> </div>
<div id="outline-container-org4e5b793" class="outline-4"> <div id="outline-container-orgf778bf1" class="outline-4">
<h4 id="org4e5b793"><span class="section-number-4">3.6.3</span> Fortran templates for front end</h4> <h4 id="orgf778bf1"><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"> <div class="outline-text-4" id="text-3-6-3">
<p> <p>
The <code>Fortran</code> templates that provide an access to the <code>C</code> API calls from Fortran. The <code>Fortran</code> templates that provide an access to the <code>C</code> API calls from Fortran.
@ -2929,8 +2929,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div> </div>
</div> </div>
<div id="outline-container-org2ed9d42" class="outline-2"> <div id="outline-container-orge3060b4" class="outline-2">
<h2 id="org2ed9d42"><span class="section-number-2">4</span> Fortran helper/wrapper functions</h2> <h2 id="orge3060b4"><span class="section-number-2">4</span> Fortran helper/wrapper functions</h2>
<div class="outline-text-2" id="text-4"> <div class="outline-text-2" id="text-4">
<p> <p>
The function below adapts the original C-based <code>trexio_open</code> for Fortran. The function below adapts the original C-based <code>trexio_open</code> for Fortran.
@ -3064,7 +3064,7 @@ two code are identical, i.e. if the <code>assert</code> statement pass.
</div> </div>
<div id="postamble" class="status"> <div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p> <p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2021-06-22 Tue 09:38</p> <p class="date">Created: 2021-06-22 Tue 10:22</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p> <p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div> </div>
</body> </body>

82
templator_hdf5.html
View File

@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head> <head>
<!-- 2021-06-22 Tue 09:38 --> <!-- 2021-06-22 Tue 10:22 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" /> <meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" /> <meta name="viewport" content="width=device-width, initial-scale=1" />
<title>HDF5 back end</title> <title>HDF5 back end</title>
@ -311,27 +311,27 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2> <h2>Table of Contents</h2>
<div id="text-table-of-contents"> <div id="text-table-of-contents">
<ul> <ul>
<li><a href="#org7ed7add">1. HDF5 back end</a> <li><a href="#orgc3d3253">1. HDF5 back end</a>
<ul> <ul>
<li><a href="#orgb592aa5">1.1. Template for HDF5 definitions</a></li> <li><a href="#orgdb2e5c8">1.1. Template for HDF5 definitions</a></li>
<li><a href="#org8e2de6f">1.2. Template for HDF5 structures</a></li> <li><a href="#org47561d9">1.2. Template for HDF5 structures</a></li>
<li><a href="#orgeeaf943">1.3. Template for HDF5 init/deinit</a></li> <li><a href="#org4835c4a">1.3. Template for HDF5 init/deinit</a></li>
<li><a href="#org6964302">1.4. Template for HDF5 has/read/write a single dimensioning variable</a></li> <li><a href="#org345f4c1">1.4. Template for HDF5 has/read/write a single dimensioning variable</a></li>
<li><a href="#org0e197f3">1.5. Template for HDF5 has/read/write a dataset of numerical data</a></li> <li><a href="#orgfbe4bec">1.5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org8833f7d">1.6. Template for HDF5 has/read/write a dataset of strings</a></li> <li><a href="#org4197b20">1.6. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org4b7d69a">1.7. Template for HDF5 has/read/write a single string attribute</a></li> <li><a href="#org2d1e0a9">1.7. Template for HDF5 has/read/write a single string attribute</a></li>
</ul> </ul>
</li> </li>
</ul> </ul>
</div> </div>
</div> </div>
<div id="outline-container-org7ed7add" class="outline-2"> <div id="outline-container-orgc3d3253" class="outline-2">
<h2 id="org7ed7add"><span class="section-number-2">1</span> HDF5 back end</h2> <h2 id="orgc3d3253"><span class="section-number-2">1</span> HDF5 back end</h2>
<div class="outline-text-2" id="text-1"> <div class="outline-text-2" id="text-1">
</div> </div>
<div id="outline-container-orgb592aa5" class="outline-3"> <div id="outline-container-orgdb2e5c8" class="outline-3">
<h3 id="orgb592aa5"><span class="section-number-3">1.1</span> Template for HDF5 definitions</h3> <h3 id="orgdb2e5c8"><span class="section-number-3">1.1</span> Template for HDF5 definitions</h3>
<div class="outline-text-3" id="text-1-1"> <div class="outline-text-3" id="text-1-1">
<div class="org-src-container"> <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> <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> </div>
<div id="outline-container-org8e2de6f" class="outline-3"> <div id="outline-container-org47561d9" class="outline-3">
<h3 id="org8e2de6f"><span class="section-number-3">1.2</span> Template for HDF5 structures</h3> <h3 id="org47561d9"><span class="section-number-3">1.2</span> Template for HDF5 structures</h3>
<div class="outline-text-3" id="text-1-2"> <div class="outline-text-3" id="text-1-2">
<div class="org-src-container"> <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> { <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> {
@ -359,8 +359,8 @@ for the JavaScript code in this tag.
</div> </div>
<div id="outline-container-orgeeaf943" class="outline-3"> <div id="outline-container-org4835c4a" class="outline-3">
<h3 id="orgeeaf943"><span class="section-number-3">1.3</span> Template for HDF5 init/deinit</h3> <h3 id="org4835c4a"><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="outline-text-3" id="text-1-3">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span> <pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -440,8 +440,8 @@ for the JavaScript code in this tag.
</div> </div>
</div> </div>
<div id="outline-container-org6964302" class="outline-3"> <div id="outline-container-org345f4c1" class="outline-3">
<h3 id="org6964302"><span class="section-number-3">1.4</span> Template for HDF5 has/read/write a single dimensioning variable</h3> <h3 id="org345f4c1"><span class="section-number-3">1.4</span> Template for HDF5 has/read/write a single dimensioning variable</h3>
<div class="outline-text-3" id="text-1-4"> <div class="outline-text-3" id="text-1-4">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span> <pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -566,8 +566,8 @@ for the JavaScript code in this tag.
</div> </div>
</div> </div>
<div id="outline-container-org0e197f3" class="outline-3"> <div id="outline-container-orgfbe4bec" class="outline-3">
<h3 id="org0e197f3"><span class="section-number-3">1.5</span> Template for HDF5 has/read/write a dataset of numerical data</h3> <h3 id="orgfbe4bec"><span class="section-number-3">1.5</span> Template for HDF5 has/read/write a dataset of numerical data</h3>
<div class="outline-text-3" id="text-1-5"> <div class="outline-text-3" id="text-1-5">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span> <pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -579,15 +579,6 @@ for the JavaScript code in this tag.
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">trexio_hdf5_t</span>* <span style="color: #a0522d;">f</span> = (<span style="color: #a020f0;">const</span> <span style="color: #228b22;">trexio_hdf5_t</span>*) file; <span style="color: #a020f0;">const</span> <span style="color: #228b22;">trexio_hdf5_t</span>* <span style="color: #a0522d;">f</span> = (<span style="color: #a020f0;">const</span> <span style="color: #228b22;">trexio_hdf5_t</span>*) file;
<span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span>;
<span style="color: #228b22;">int</span> <span style="color: #a0522d;">rrank</span>;
// <span style="color: #b22222;">get the rank of the dataset in a file</span>
status = H5LTget_dataset_ndims (f-&gt;$group$_group, $GROUP_DSET$_NAME, &amp;rrank);
<span style="color: #a020f0;">if</span> (status &lt; 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
<span style="color: #a020f0;">if</span> (rrank != (<span style="color: #228b22;">int</span>) rank) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_3;
// <span style="color: #b22222;">open the dataset to get its dimensions</span> // <span style="color: #b22222;">open the dataset to get its dimensions</span>
<span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dset_id</span> = H5Dopen(f-&gt;$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT); <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dset_id</span> = H5Dopen(f-&gt;$group$_group, $GROUP_DSET$_NAME, H5P_DEFAULT);
<span style="color: #a020f0;">if</span> (dset_id &lt;= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID; <span style="color: #a020f0;">if</span> (dset_id &lt;= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
@ -596,25 +587,34 @@ for the JavaScript code in this tag.
<span style="color: #228b22;">hsize_t</span>* <span style="color: #a0522d;">ddims</span> = CALLOC( (<span style="color: #228b22;">int</span>) rank, hsize_t); <span style="color: #228b22;">hsize_t</span>* <span style="color: #a0522d;">ddims</span> = CALLOC( (<span style="color: #228b22;">int</span>) rank, hsize_t);
<span style="color: #a020f0;">if</span> (ddims == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_FAILURE; <span style="color: #a020f0;">if</span> (ddims == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
// <span style="color: #b22222;">read dimensions from the existing dataset</span> // <span style="color: #b22222;">get the dataspace of the dataset</span>
status = H5LDget_dset_dims(dset_id, ddims); <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dspace_id</span> = H5Dget_space(dset_id);
// <span style="color: #b22222;">get the rank and dimensions of the dataset</span>
<span style="color: #228b22;">int</span> <span style="color: #a0522d;">rrank</span> = H5Sget_simple_extent_dims(dspace_id, ddims, <span style="color: #008b8b;">NULL</span>);
H5Dclose(dset_id); // <span style="color: #b22222;">check that dimensions are consistent</span>
<span style="color: #a020f0;">if</span> (status &lt; 0) { <span style="color: #a020f0;">if</span> (rrank != (<span style="color: #228b22;">int</span>) rank) {
FREE(ddims); FREE(ddims);
<span style="color: #a020f0;">return</span> TREXIO_FAILURE; H5Sclose(dspace_id);
H5Dclose(dset_id);
<span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_3;
} }
<span style="color: #a020f0;">for</span> (<span style="color: #228b22;">uint32_t</span> <span style="color: #a0522d;">i</span>=0; i&lt;rank; ++i){ <span style="color: #a020f0;">for</span> (<span style="color: #228b22;">uint32_t</span> <span style="color: #a0522d;">i</span>=0; i&lt;rank; ++i){
<span style="color: #a020f0;">if</span> (ddims[i] != dims[i]) { <span style="color: #a020f0;">if</span> (ddims[i] != dims[i]) {
FREE(ddims); FREE(ddims);
H5Sclose(dspace_id);
H5Dclose(dset_id);
<span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_4; <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_4;
} }
} }
FREE(ddims); FREE(ddims);
H5Sclose(dspace_id);
H5Dclose(dset_id);
/* <span style="color: #b22222;">High-level H5LT API. No need to deal with dataspaces and datatypes </span>*/ /* <span style="color: #b22222;">High-level H5LT API. No need to deal with dataspaces and datatypes </span>*/
status = H5LTread_dataset(f-&gt;$group$_group, <span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5LTread_dataset(f-&gt;$group$_group,
$GROUP_DSET$_NAME, $GROUP_DSET$_NAME,
H5T_$GROUP_DSET_H5_DTYPE$, H5T_$GROUP_DSET_H5_DTYPE$,
$group_dset$); $group_dset$);
@ -696,8 +696,8 @@ for the JavaScript code in this tag.
</div> </div>
</div> </div>
<div id="outline-container-org8833f7d" class="outline-3"> <div id="outline-container-org4197b20" class="outline-3">
<h3 id="org8833f7d"><span class="section-number-3">1.6</span> Template for HDF5 has/read/write a dataset of strings</h3> <h3 id="org4197b20"><span class="section-number-3">1.6</span> Template for HDF5 has/read/write a dataset of strings</h3>
<div class="outline-text-3" id="text-1-6"> <div class="outline-text-3" id="text-1-6">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span> <pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -901,8 +901,8 @@ for the JavaScript code in this tag.
</div> </div>
</div> </div>
<div id="outline-container-org4b7d69a" class="outline-3"> <div id="outline-container-org2d1e0a9" class="outline-3">
<h3 id="org4b7d69a"><span class="section-number-3">1.7</span> Template for HDF5 has/read/write a single string attribute</h3> <h3 id="org2d1e0a9"><span class="section-number-3">1.7</span> Template for HDF5 has/read/write a single string attribute</h3>
<div class="outline-text-3" id="text-1-7"> <div class="outline-text-3" id="text-1-7">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span> <pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1029,7 +1029,7 @@ for the JavaScript code in this tag.
</div> </div>
<div id="postamble" class="status"> <div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p> <p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2021-06-22 Tue 09:38</p> <p class="date">Created: 2021-06-22 Tue 10:22</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p> <p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div> </div>
</body> </body>

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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head> <head>
<!-- 2021-06-22 Tue 09:38 --> <!-- 2021-06-22 Tue 10:22 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" /> <meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" /> <meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TEXT back end</title> <title>TEXT back end</title>
@ -311,26 +311,26 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2> <h2>Table of Contents</h2>
<div id="text-table-of-contents"> <div id="text-table-of-contents">
<ul> <ul>
<li><a href="#org3fd98b9">1. TEXT back end</a> <li><a href="#org6980a1d">1. TEXT back end</a>
<ul> <ul>
<li><a href="#org2b28751">1.1. Template for group-related structures in text back end</a></li> <li><a href="#org4a956e8">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#org0fa5d40">1.2. Template for general structure in text back end</a></li> <li><a href="#org1986736">1.2. Template for general structure in text back end</a></li>
<li><a href="#orgd164eb2">1.3. Initialize function (constant part)</a></li> <li><a href="#org94ad673">1.3. Initialize function (constant part)</a></li>
<li><a href="#org8349fdb">1.4. Deinitialize function (templated part)</a></li> <li><a href="#orgf20c903">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#orga48b304">1.5. Template for text read struct</a></li> <li><a href="#org948bec8">1.5. Template for text read struct</a></li>
<li><a href="#orgade1e1a">1.6. Template for text flush struct</a></li> <li><a href="#orgfe865f3">1.6. Template for text flush struct</a></li>
<li><a href="#orgba86f14">1.7. Template for text free memory</a></li> <li><a href="#org0485fc6">1.7. Template for text free memory</a></li>
<li><a href="#org293c636">1.8. Template for has/read/write the num attribute</a></li> <li><a href="#org471f17d">1.8. Template for has/read/write the num attribute</a></li>
<li><a href="#orgf8456b5">1.9. Template for has/read/write the dataset of numerical data</a></li> <li><a href="#orgd83b77c">1.9. Template for has/read/write the dataset of numerical data</a></li>
<li><a href="#org923274d">1.10. Template for has/read/write the dataset of strings</a></li> <li><a href="#orgbc536fa">1.10. Template for has/read/write the dataset of strings</a></li>
<li><a href="#orgf8616d9">1.11. Template for has/read/write the string attribute</a></li> <li><a href="#orga7e1cd1">1.11. Template for has/read/write the string attribute</a></li>
<li><a href="#orga724830">1.12. RDM struct (hard-coded)</a> <li><a href="#orgbe0f5b4">1.12. RDM struct (hard-coded)</a>
<ul> <ul>
<li><a href="#orga449ff7">1.12.1. Read the complete struct</a></li> <li><a href="#org9ffc8b3">1.12.1. Read the complete struct</a></li>
<li><a href="#org5b97036">1.12.2. Flush the complete struct</a></li> <li><a href="#org0173c0a">1.12.2. Flush the complete struct</a></li>
<li><a href="#org6e145f7">1.12.3. Free memory</a></li> <li><a href="#org3e69bab">1.12.3. Free memory</a></li>
<li><a href="#org6290709">1.12.4. Read/Write the one<sub>e</sub> attribute</a></li> <li><a href="#org3e05553">1.12.4. Read/Write the one<sub>e</sub> attribute</a></li>
<li><a href="#org0c3ea24">1.12.5. Read/Write the two<sub>e</sub> attribute</a></li> <li><a href="#orgd901aa8">1.12.5. Read/Write the two<sub>e</sub> attribute</a></li>
</ul> </ul>
</li> </li>
</ul> </ul>
@ -339,8 +339,8 @@ for the JavaScript code in this tag.
</div> </div>
</div> </div>
<div id="outline-container-org3fd98b9" class="outline-2"> <div id="outline-container-org6980a1d" class="outline-2">
<h2 id="org3fd98b9"><span class="section-number-2">1</span> TEXT back end</h2> <h2 id="org6980a1d"><span class="section-number-2">1</span> TEXT back end</h2>
<div class="outline-text-2" id="text-1"> <div class="outline-text-2" id="text-1">
<p> <p>
The "file" produced by the text back end is a directory with one 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> </p>
</div> </div>
<div id="outline-container-org2b28751" class="outline-3"> <div id="outline-container-org4a956e8" class="outline-3">
<h3 id="org2b28751"><span class="section-number-3">1.1</span> Template for group-related structures in text back end</h3> <h3 id="org4a956e8"><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="outline-text-3" id="text-1-1">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> $group$_s { <pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> $group$_s {
@ -380,8 +380,8 @@ The file is written when closed, or when the flush function is called.
</div> </div>
</div> </div>
<div id="outline-container-org0fa5d40" class="outline-3"> <div id="outline-container-org1986736" class="outline-3">
<h3 id="org0fa5d40"><span class="section-number-3">1.2</span> Template for general structure in text back end</h3> <h3 id="org1986736"><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="outline-text-3" id="text-1-2">
<div class="org-src-container"> <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> { <pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #a020f0;">struct</span> <span style="color: #228b22;">rdm_s</span> {
@ -407,8 +407,8 @@ The file is written when closed, or when the flush function is called.
</div> </div>
</div> </div>
<div id="outline-container-orgd164eb2" class="outline-3"> <div id="outline-container-org94ad673" class="outline-3">
<h3 id="orgd164eb2"><span class="section-number-3">1.3</span> Initialize function (constant part)</h3> <h3 id="org94ad673"><span class="section-number-3">1.3</span> Initialize function (constant part)</h3>
<div class="outline-text-3" id="text-1-3"> <div class="outline-text-3" id="text-1-3">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span> <pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -509,8 +509,8 @@ The file is written when closed, or when the flush function is called.
</div> </div>
</div> </div>
<div id="outline-container-org8349fdb" class="outline-3"> <div id="outline-container-orgf20c903" class="outline-3">
<h3 id="org8349fdb"><span class="section-number-3">1.4</span> Deinitialize function (templated part)</h3> <h3 id="orgf20c903"><span class="section-number-3">1.4</span> Deinitialize function (templated part)</h3>
<div class="outline-text-3" id="text-1-4"> <div class="outline-text-3" id="text-1-4">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span> <pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -535,8 +535,8 @@ The file is written when closed, or when the flush function is called.
</div> </div>
</div> </div>
<div id="outline-container-orga48b304" class="outline-3"> <div id="outline-container-org948bec8" class="outline-3">
<h3 id="orga48b304"><span class="section-number-3">1.5</span> Template for text read struct</h3> <h3 id="org948bec8"><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="outline-text-3" id="text-1-5">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-c">$group$_t* <pre class="src src-c">$group$_t*
@ -807,8 +807,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div> </div>
</div> </div>
<div id="outline-container-orgade1e1a" class="outline-3"> <div id="outline-container-orgfe865f3" class="outline-3">
<h3 id="orgade1e1a"><span class="section-number-3">1.6</span> Template for text flush struct</h3> <h3 id="orgfe865f3"><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="outline-text-3" id="text-1-6">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span> <pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -872,8 +872,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div> </div>
</div> </div>
<div id="outline-container-orgba86f14" class="outline-3"> <div id="outline-container-org0485fc6" class="outline-3">
<h3 id="orgba86f14"><span class="section-number-3">1.7</span> Template for text free memory</h3> <h3 id="org0485fc6"><span class="section-number-3">1.7</span> Template for text free memory</h3>
<div class="outline-text-3" id="text-1-7"> <div class="outline-text-3" id="text-1-7">
<p> <p>
Memory is allocated when reading. The following function frees memory. Memory is allocated when reading. The following function frees memory.
@ -918,8 +918,8 @@ Memory is allocated when reading. The following function frees memory.
</div> </div>
</div> </div>
<div id="outline-container-org293c636" class="outline-3"> <div id="outline-container-org471f17d" class="outline-3">
<h3 id="org293c636"><span class="section-number-3">1.8</span> Template for has/read/write the num attribute</h3> <h3 id="org471f17d"><span class="section-number-3">1.8</span> Template for has/read/write the num attribute</h3>
<div class="outline-text-3" id="text-1-8"> <div class="outline-text-3" id="text-1-8">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span> <pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -981,8 +981,8 @@ Memory is allocated when reading. The following function frees memory.
</div> </div>
</div> </div>
<div id="outline-container-orgf8456b5" class="outline-3"> <div id="outline-container-orgd83b77c" class="outline-3">
<h3 id="orgf8456b5"><span class="section-number-3">1.9</span> Template for has/read/write the dataset of numerical data</h3> <h3 id="orgd83b77c"><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"> <div class="outline-text-3" id="text-1-9">
<p> <p>
The <code>group_dset</code> array is assumed allocated with the appropriate size. The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1078,8 +1078,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-org923274d" class="outline-3"> <div id="outline-container-orgbc536fa" class="outline-3">
<h3 id="org923274d"><span class="section-number-3">1.10</span> Template for has/read/write the dataset of strings</h3> <h3 id="orgbc536fa"><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"> <div class="outline-text-3" id="text-1-10">
<p> <p>
The <code>group_dset</code> array is assumed allocated with the appropriate size. The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1181,8 +1181,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-orgf8616d9" class="outline-3"> <div id="outline-container-orga7e1cd1" class="outline-3">
<h3 id="orgf8616d9"><span class="section-number-3">1.11</span> Template for has/read/write the string attribute</h3> <h3 id="orga7e1cd1"><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="outline-text-3" id="text-1-11">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span> <pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1256,12 +1256,12 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div> </div>
</div> </div>
</div> </div>
<div id="outline-container-orga724830" class="outline-3"> <div id="outline-container-orgbe0f5b4" class="outline-3">
<h3 id="orga724830"><span class="section-number-3">1.12</span> RDM struct (hard-coded)</h3> <h3 id="orgbe0f5b4"><span class="section-number-3">1.12</span> RDM struct (hard-coded)</h3>
<div class="outline-text-3" id="text-1-12"> <div class="outline-text-3" id="text-1-12">
</div> </div>
<div id="outline-container-orga449ff7" class="outline-4"> <div id="outline-container-org9ffc8b3" class="outline-4">
<h4 id="orga449ff7"><span class="section-number-4">1.12.1</span> Read the complete struct</h4> <h4 id="org9ffc8b3"><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="outline-text-4" id="text-1-12-1">
<div class="org-src-container"> <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>); <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>);
@ -1356,8 +1356,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div> </div>
</div> </div>
<div id="outline-container-org5b97036" class="outline-4"> <div id="outline-container-org0173c0a" class="outline-4">
<h4 id="org5b97036"><span class="section-number-4">1.12.2</span> Flush the complete struct</h4> <h4 id="org0173c0a"><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="outline-text-4" id="text-1-12-2">
<div class="org-src-container"> <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>); <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>);
@ -1399,8 +1399,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div> </div>
</div> </div>
<div id="outline-container-org6e145f7" class="outline-4"> <div id="outline-container-org3e69bab" class="outline-4">
<h4 id="org6e145f7"><span class="section-number-4">1.12.3</span> Free memory</h4> <h4 id="org3e69bab"><span class="section-number-4">1.12.3</span> Free memory</h4>
<div class="outline-text-4" id="text-1-12-3"> <div class="outline-text-4" id="text-1-12-3">
<p> <p>
Memory is allocated when reading. The followig function frees memory. Memory is allocated when reading. The followig function frees memory.
@ -1436,8 +1436,8 @@ Memory is allocated when reading. The followig function frees memory.
</div> </div>
</div> </div>
<div id="outline-container-org6290709" class="outline-4"> <div id="outline-container-org3e05553" class="outline-4">
<h4 id="org6290709"><span class="section-number-4">1.12.4</span> Read/Write the one<sub>e</sub> attribute</h4> <h4 id="org3e05553"><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"> <div class="outline-text-4" id="text-1-12-4">
<p> <p>
The <code>one_e</code> array is assumed allocated with the appropriate size. The <code>one_e</code> array is assumed allocated with the appropriate size.
@ -1503,8 +1503,8 @@ The <code>one_e</code> array is assumed allocated with the appropriate size.
</div> </div>
</div> </div>
<div id="outline-container-org0c3ea24" class="outline-4"> <div id="outline-container-orgd901aa8" class="outline-4">
<h4 id="org0c3ea24"><span class="section-number-4">1.12.5</span> Read/Write the two<sub>e</sub> attribute</h4> <h4 id="orgd901aa8"><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"> <div class="outline-text-4" id="text-1-12-5">
<p> <p>
<code>two_e</code> is a sparse data structure, which can be too large to fit <code>two_e</code> is a sparse data structure, which can be too large to fit
@ -1612,7 +1612,7 @@ file for each sparse float structure.
</div> </div>
<div id="postamble" class="status"> <div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p> <p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2021-06-22 Tue 09:38</p> <p class="date">Created: 2021-06-22 Tue 10:22</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p> <p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div> </div>
</body> </body>

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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"> <html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head> <head>
<!-- 2021-06-22 Tue 09:38 --> <!-- 2021-06-22 Tue 10:22 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" /> <meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" /> <meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREX Configuration file</title> <title>TREX Configuration file</title>
@ -333,28 +333,28 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2> <h2>Table of Contents</h2>
<div id="text-table-of-contents"> <div id="text-table-of-contents">
<ul> <ul>
<li><a href="#orgb368b60">1. Metadata</a></li> <li><a href="#org5279cdc">1. Metadata</a></li>
<li><a href="#org60acf64">2. Electron</a></li> <li><a href="#org0982faa">2. Electron</a></li>
<li><a href="#org29e5d50">3. Nucleus</a></li> <li><a href="#org06148c9">3. Nucleus</a></li>
<li><a href="#org8807ecf">4. <span class="todo TODO">TODO</span> Effective core potentials</a></li> <li><a href="#org1091334">4. <span class="todo TODO">TODO</span> Effective core potentials</a></li>
<li><a href="#org4068d17">5. Basis set</a></li> <li><a href="#orgd468ddf">5. Basis set</a></li>
<li><a href="#org68edbeb">6. Atomic orbitals</a> <li><a href="#orgbd99e35">6. Atomic orbitals</a>
<ul> <ul>
<li><a href="#ao_one_e">6.1. One-electron integrals</a></li> <li><a href="#ao_one_e">6.1. One-electron integrals</a></li>
<li><a href="#ao_two_e">6.2. Two-electron integrals</a></li> <li><a href="#ao_two_e">6.2. Two-electron integrals</a></li>
</ul> </ul>
</li> </li>
<li><a href="#orgbd8f27f">7. Molecular orbitals</a> <li><a href="#org80705e6">7. Molecular orbitals</a>
<ul> <ul>
<li><a href="#org0993734">7.1. One-electron integrals</a></li> <li><a href="#org887cd83">7.1. One-electron integrals</a></li>
<li><a href="#org5995ec2">7.2. Two-electron integrals</a></li> <li><a href="#orgf9a83b3">7.2. Two-electron integrals</a></li>
</ul> </ul>
</li> </li>
<li><a href="#orgf22ed86">8. <span class="todo TODO">TODO</span> Slater determinants</a></li> <li><a href="#org7ec2323">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#org70342c9">9. <span class="todo TODO">TODO</span> Reduced density matrices</a></li> <li><a href="#org067a381">9. <span class="todo TODO">TODO</span> Reduced density matrices</a></li>
<li><a href="#org73f11b4">10. Appendix</a> <li><a href="#orgba9a827">10. Appendix</a>
<ul> <ul>
<li><a href="#org4361076">10.1. Python script from table to json</a></li> <li><a href="#org7facd3c">10.1. Python script from table to json</a></li>
</ul> </ul>
</li> </li>
</ul> </ul>
@ -379,8 +379,8 @@ arrays are 0-base. Hence, we introduce the <code>index</code> type which is an
</pre> </pre>
</div> </div>
<div id="outline-container-orgb368b60" class="outline-2"> <div id="outline-container-org5279cdc" class="outline-2">
<h2 id="orgb368b60"><span class="section-number-2">1</span> Metadata</h2> <h2 id="org5279cdc"><span class="section-number-2">1</span> Metadata</h2>
<div class="outline-text-2" id="text-1"> <div class="outline-text-2" id="text-1">
<p> <p>
As we expect our files to be archived in open-data repositories, we As we expect our files to be archived in open-data repositories, we
@ -390,7 +390,7 @@ which have participated to the creation of the file, a list of
authors of the file, and a textual description. authors of the file, and a textual description.
</p> </p>
<table id="orgdfb49e5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides"> <table id="orgdd683e1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup> <colgroup>
@ -442,15 +442,15 @@ authors of the file, and a textual description.
</div> </div>
</div> </div>
<div id="outline-container-org60acf64" class="outline-2"> <div id="outline-container-org0982faa" class="outline-2">
<h2 id="org60acf64"><span class="section-number-2">2</span> Electron</h2> <h2 id="org0982faa"><span class="section-number-2">2</span> Electron</h2>
<div class="outline-text-2" id="text-2"> <div class="outline-text-2" id="text-2">
<p> <p>
We consider wave functions expressed in the spin-free formalism, where We consider wave functions expressed in the spin-free formalism, where
the number of &uarr; and &darr; electrons is fixed. the number of &uarr; and &darr; electrons is fixed.
</p> </p>
<table id="org7d59a0f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides"> <table id="org55d80d1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup> <colgroup>
@ -481,15 +481,15 @@ the number of &uarr; and &darr; electrons is fixed.
</div> </div>
</div> </div>
<div id="outline-container-org29e5d50" class="outline-2"> <div id="outline-container-org06148c9" class="outline-2">
<h2 id="org29e5d50"><span class="section-number-2">3</span> Nucleus</h2> <h2 id="org06148c9"><span class="section-number-2">3</span> Nucleus</h2>
<div class="outline-text-2" id="text-3"> <div class="outline-text-2" id="text-3">
<p> <p>
The nuclei are considered as fixed point charges. Coordinates are The nuclei are considered as fixed point charges. Coordinates are
given in Cartesian \((x,y,z)\) format. given in Cartesian \((x,y,z)\) format.
</p> </p>
<table id="org2b93ada" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides"> <table id="org88f35a6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup> <colgroup>
@ -541,8 +541,8 @@ given in Cartesian \((x,y,z)\) format.
</div> </div>
</div> </div>
<div id="outline-container-org8807ecf" class="outline-2"> <div id="outline-container-org1091334" class="outline-2">
<h2 id="org8807ecf"><span class="section-number-2">4</span> <span class="todo TODO">TODO</span> Effective core potentials</h2> <h2 id="org1091334"><span class="section-number-2">4</span> <span class="todo TODO">TODO</span> Effective core potentials</h2>
<div class="outline-text-2" id="text-4"> <div class="outline-text-2" id="text-4">
<p> <p>
An effective core potential (ECP) \(V_A^{\text{pp}}\) replacing the An effective core potential (ECP) \(V_A^{\text{pp}}\) replacing the
@ -587,7 +587,7 @@ letters are parameters.
<li>\(\hat{V}_\text{ecp,nl} = \sum_A \hat{V}_A^{\text{nl}}\) : non-local component</li> <li>\(\hat{V}_\text{ecp,nl} = \sum_A \hat{V}_A^{\text{nl}}\) : non-local component</li>
</ul> </ul>
<table id="org8c66a86" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides"> <table id="org2b19107" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup> <colgroup>
@ -688,8 +688,8 @@ letters are parameters.
</div> </div>
</div> </div>
<div id="outline-container-org4068d17" class="outline-2"> <div id="outline-container-orgd468ddf" class="outline-2">
<h2 id="org4068d17"><span class="section-number-2">5</span> Basis set</h2> <h2 id="orgd468ddf"><span class="section-number-2">5</span> Basis set</h2>
<div class="outline-text-2" id="text-5"> <div class="outline-text-2" id="text-5">
<p> <p>
We consider here basis functions centered on nuclei. Hence, we enable We consider here basis functions centered on nuclei. Hence, we enable
@ -742,7 +742,7 @@ If the the basis function is not considered normalized, \(\mathcal{N}_s=1\).
All the basis set parameters are stored in one-dimensional arrays: All the basis set parameters are stored in one-dimensional arrays:
</p> </p>
<table id="org5f224fc" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides"> <table id="orge01baf1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup> <colgroup>
@ -903,8 +903,8 @@ prim_factor =
</div> </div>
</div> </div>
<div id="outline-container-org68edbeb" class="outline-2"> <div id="outline-container-orgbd99e35" class="outline-2">
<h2 id="org68edbeb"><span class="section-number-2">6</span> Atomic orbitals</h2> <h2 id="orgbd99e35"><span class="section-number-2">6</span> Atomic orbitals</h2>
<div class="outline-text-2" id="text-6"> <div class="outline-text-2" id="text-6">
<p> <p>
Going from the atomic basis set to AOs implies a systematic Going from the atomic basis set to AOs implies a systematic
@ -952,13 +952,13 @@ shell, as in the GAMESS convention where
<p> <p>
In such a case, one should set the normalization of the shell (in In such a case, one should set the normalization of the shell (in
the <a href="#org4068d17">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the the <a href="#orgd468ddf">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
normalization factor of the atomic orbitals in spherical coordinates. normalization factor of the atomic orbitals in spherical coordinates.
The normalization factor of the \(xy\) function which should be The normalization factor of the \(xy\) function which should be
introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\). introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
</p> </p>
<table id="org1281a3a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides"> <table id="org339cf8f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup> <colgroup>
@ -1002,8 +1002,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
</table> </table>
</div> </div>
<div id="outline-container-org4860eeb" class="outline-3"> <div id="outline-container-orgee50798" class="outline-3">
<h3 id="ao_one_e"><a id="org4860eeb"></a><span class="section-number-3">6.1</span> One-electron integrals</h3> <h3 id="ao_one_e"><a id="orgee50798"></a><span class="section-number-3">6.1</span> One-electron integrals</h3>
<div class="outline-text-3" id="text-ao_one_e"> <div class="outline-text-3" id="text-ao_one_e">
<ul class="org-ul"> <ul class="org-ul">
<li>\[ \hat{V}_{\text{ne}} = \sum_{A=1}^{N_\text{nucl}} <li>\[ \hat{V}_{\text{ne}} = \sum_{A=1}^{N_\text{nucl}}
@ -1021,7 +1021,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals. over atomic orbitals.
</p> </p>
<table id="orgebd22a1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides"> <table id="orgdfd2e58" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup> <colgroup>
@ -1080,8 +1080,8 @@ over atomic orbitals.
</div> </div>
</div> </div>
<div id="outline-container-org0c4183e" class="outline-3"> <div id="outline-container-orgf29d729" class="outline-3">
<h3 id="ao_two_e"><a id="org0c4183e"></a><span class="section-number-3">6.2</span> Two-electron integrals</h3> <h3 id="ao_two_e"><a id="orgf29d729"></a><span class="section-number-3">6.2</span> Two-electron integrals</h3>
<div class="outline-text-3" id="text-ao_two_e"> <div class="outline-text-3" id="text-ao_two_e">
<p> <p>
The two-electron integrals for a two-electron operator \(\hat{O}\) are The two-electron integrals for a two-electron operator \(\hat{O}\) are
@ -1102,7 +1102,7 @@ notation.
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li> \mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
</ul> </ul>
<table id="org3ee726a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides"> <table id="org0b07b1e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup> <colgroup>
@ -1134,10 +1134,10 @@ notation.
</div> </div>
</div> </div>
<div id="outline-container-orgbd8f27f" class="outline-2"> <div id="outline-container-org80705e6" class="outline-2">
<h2 id="orgbd8f27f"><span class="section-number-2">7</span> Molecular orbitals</h2> <h2 id="org80705e6"><span class="section-number-2">7</span> Molecular orbitals</h2>
<div class="outline-text-2" id="text-7"> <div class="outline-text-2" id="text-7">
<table id="orgf678ad2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides"> <table id="org0334a09" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup> <colgroup>
@ -1195,8 +1195,8 @@ notation.
</table> </table>
</div> </div>
<div id="outline-container-org0993734" class="outline-3"> <div id="outline-container-org887cd83" class="outline-3">
<h3 id="org0993734"><span class="section-number-3">7.1</span> One-electron integrals</h3> <h3 id="org887cd83"><span class="section-number-3">7.1</span> One-electron integrals</h3>
<div class="outline-text-3" id="text-7-1"> <div class="outline-text-3" id="text-7-1">
<p> <p>
The operators as the same as those defined in the The operators as the same as those defined in the
@ -1204,7 +1204,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals. the basis of molecular orbitals.
</p> </p>
<table id="org9894a94" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides"> <table id="org5a122f1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup> <colgroup>
@ -1263,8 +1263,8 @@ the basis of molecular orbitals.
</div> </div>
</div> </div>
<div id="outline-container-org5995ec2" class="outline-3"> <div id="outline-container-orgf9a83b3" class="outline-3">
<h3 id="org5995ec2"><span class="section-number-3">7.2</span> Two-electron integrals</h3> <h3 id="orgf9a83b3"><span class="section-number-3">7.2</span> Two-electron integrals</h3>
<div class="outline-text-3" id="text-7-2"> <div class="outline-text-3" id="text-7-2">
<p> <p>
The operators as the same as those defined in the The operators as the same as those defined in the
@ -1272,7 +1272,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals. the basis of molecular orbitals.
</p> </p>
<table id="org86973d3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides"> <table id="org6886615" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup> <colgroup>
@ -1304,13 +1304,13 @@ the basis of molecular orbitals.
</div> </div>
</div> </div>
<div id="outline-container-orgf22ed86" class="outline-2"> <div id="outline-container-org7ec2323" class="outline-2">
<h2 id="orgf22ed86"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2> <h2 id="org7ec2323"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
</div> </div>
<div id="outline-container-org70342c9" class="outline-2"> <div id="outline-container-org067a381" class="outline-2">
<h2 id="org70342c9"><span class="section-number-2">9</span> <span class="todo TODO">TODO</span> Reduced density matrices</h2> <h2 id="org067a381"><span class="section-number-2">9</span> <span class="todo TODO">TODO</span> Reduced density matrices</h2>
<div class="outline-text-2" id="text-9"> <div class="outline-text-2" id="text-9">
<table id="org115672d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides"> <table id="org8158e45" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup> <colgroup>
@ -1349,15 +1349,15 @@ the basis of molecular orbitals.
</div> </div>
</div> </div>
<div id="outline-container-org73f11b4" class="outline-2"> <div id="outline-container-orgba9a827" class="outline-2">
<h2 id="org73f11b4"><span class="section-number-2">10</span> Appendix</h2> <h2 id="orgba9a827"><span class="section-number-2">10</span> Appendix</h2>
<div class="outline-text-2" id="text-10"> <div class="outline-text-2" id="text-10">
</div> </div>
<div id="outline-container-org4361076" class="outline-3"> <div id="outline-container-org7facd3c" class="outline-3">
<h3 id="org4361076"><span class="section-number-3">10.1</span> Python script from table to json</h3> <h3 id="org7facd3c"><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="outline-text-3" id="text-10-1">
<div class="org-src-container"> <div class="org-src-container">
<pre class="src src-python" id="orgc173253"><span style="color: #a020f0;">print</span>(<span style="color: #8b2252;">"""#+begin_src python :tangle trex.json"""</span>) <pre class="src src-python" id="orgd0f52f2"><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: #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;">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 <span style="color: #a0522d;">f1</span> = 0 ; <span style="color: #a0522d;">f2</span> = 0 ; <span style="color: #a0522d;">f3</span> = 0
@ -1416,7 +1416,7 @@ the basis of molecular orbitals.
</div> </div>
<div id="postamble" class="status"> <div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p> <p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2021-06-22 Tue 09:38</p> <p class="date">Created: 2021-06-22 Tue 10:22</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p> <p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div> </div>
</body> </body>