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scemama 2021-11-02 10:53:25 +00:00
parent 56e8d15cbd
commit 1be9bd3220
7 changed files with 491 additions and 349 deletions

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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>
<!-- 2021-11-01 Mon 10:44 -->
<!-- 2021-11-02 Tue 10:53 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title>
@ -343,7 +343,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2021-11-01 Mon 10:44</p>
<p class="date">Created: 2021-11-02 Tue 10:53</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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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>
<!-- 2021-11-01 Mon 10:44 -->
<!-- 2021-11-02 Tue 10:53 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>&lrm;</title>
@ -232,8 +232,8 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org909961f">1. Text back end</a></li>
<li><a href="#orga9ab817">2. HDF5 Back end</a></li>
<li><a href="#orgac099a4">1. Text back end</a></li>
<li><a href="#org8a19ecb">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-org909961f" class="outline-2">
<h2 id="org909961f"><span class="section-number-2">1</span> Text back end</h2>
<div id="outline-container-orgac099a4" class="outline-2">
<h2 id="orgac099a4"><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-orga9ab817" class="outline-2">
<h2 id="orga9ab817"><span class="section-number-2">2</span> HDF5 Back end</h2>
<div id="outline-container-org8a19ecb" class="outline-2">
<h2 id="org8a19ecb"><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: 2021-11-01 Mon 10:44</p>
<p class="date">Created: 2021-11-02 Tue 10:53</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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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>
<!-- 2021-11-01 Mon 10:44 -->
<!-- 2021-11-02 Tue 10:53 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title>
@ -343,7 +343,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2021-11-01 Mon 10:44</p>
<p class="date">Created: 2021-11-02 Tue 10:53</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2021-11-01 Mon 10:44 -->
<!-- 2021-11-02 Tue 10:53 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>HDF5 back end</title>
@ -311,27 +311,27 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org0ffc474">1. HDF5 back end</a>
<li><a href="#org8ed0d04">1. HDF5 back end</a>
<ul>
<li><a href="#org304457d">1.1. Template for HDF5 definitions</a></li>
<li><a href="#orgff2cba2">1.2. Template for HDF5 structures</a></li>
<li><a href="#orgc3e416a">1.3. Template for HDF5 init/deinit</a></li>
<li><a href="#org8432eab">1.4. Template for HDF5 has/read/write the numerical attribute</a></li>
<li><a href="#orgb3df0cf">1.5. Template for HDF5 has/read/write the dataset of numerical data</a></li>
<li><a href="#orgbffa601">1.6. Template for HDF5 has/read/write the dataset of strings</a></li>
<li><a href="#org8c247da">1.7. Template for HDF5 has/read/write the string attribute</a></li>
<li><a href="#orgd36e9ed">1.1. Template for HDF5 definitions</a></li>
<li><a href="#orgb55a59f">1.2. Template for HDF5 structures</a></li>
<li><a href="#orgf2406a1">1.3. Template for HDF5 init/deinit</a></li>
<li><a href="#org3b96856">1.4. Template for HDF5 has/read/write the numerical attribute</a></li>
<li><a href="#org7e8c8d9">1.5. Template for HDF5 has/read/write the dataset of numerical data</a></li>
<li><a href="#org551def5">1.6. Template for HDF5 has/read/write the dataset of strings</a></li>
<li><a href="#org962556b">1.7. Template for HDF5 has/read/write the string attribute</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org0ffc474" class="outline-2">
<h2 id="org0ffc474"><span class="section-number-2">1</span> HDF5 back end</h2>
<div id="outline-container-org8ed0d04" class="outline-2">
<h2 id="org8ed0d04"><span class="section-number-2">1</span> HDF5 back end</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-org304457d" class="outline-3">
<h3 id="org304457d"><span class="section-number-3">1.1</span> Template for HDF5 definitions</h3>
<div id="outline-container-orgd36e9ed" class="outline-3">
<h3 id="orgd36e9ed"><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-orgff2cba2" class="outline-3">
<h3 id="orgff2cba2"><span class="section-number-3">1.2</span> Template for HDF5 structures</h3>
<div id="outline-container-orgb55a59f" class="outline-3">
<h3 id="orgb55a59f"><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-orgc3e416a" class="outline-3">
<h3 id="orgc3e416a"><span class="section-number-3">1.3</span> Template for HDF5 init/deinit</h3>
<div id="outline-container-orgf2406a1" class="outline-3">
<h3 id="orgf2406a1"><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-org8432eab" class="outline-3">
<h3 id="org8432eab"><span class="section-number-3">1.4</span> Template for HDF5 has/read/write the numerical attribute</h3>
<div id="outline-container-org3b96856" class="outline-3">
<h3 id="org3b96856"><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-orgb3df0cf" class="outline-3">
<h3 id="orgb3df0cf"><span class="section-number-3">1.5</span> Template for HDF5 has/read/write the dataset of numerical data</h3>
<div id="outline-container-org7e8c8d9" class="outline-3">
<h3 id="org7e8c8d9"><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-orgbffa601" class="outline-3">
<h3 id="orgbffa601"><span class="section-number-3">1.6</span> Template for HDF5 has/read/write the dataset of strings</h3>
<div id="outline-container-org551def5" class="outline-3">
<h3 id="org551def5"><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-org8c247da" class="outline-3">
<h3 id="org8c247da"><span class="section-number-3">1.7</span> Template for HDF5 has/read/write the string attribute</h3>
<div id="outline-container-org962556b" class="outline-3">
<h3 id="org962556b"><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: 2021-11-01 Mon 10:44</p>
<p class="date">Created: 2021-11-02 Tue 10:53</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2021-11-01 Mon 10:44 -->
<!-- 2021-11-02 Tue 10:53 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TEXT back end</title>
@ -311,26 +311,26 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgc9c5222">1. TEXT back end</a>
<li><a href="#org613b8a8">1. TEXT back end</a>
<ul>
<li><a href="#orgdfdd100">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#orgc72bc6f">1.2. Template for general structure in text back end</a></li>
<li><a href="#org6d3d5ff">1.3. Initialize function (constant part)</a></li>
<li><a href="#org84327ec">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#orgab721df">1.5. Template for text read struct</a></li>
<li><a href="#org1e1041a">1.6. Template for text flush struct</a></li>
<li><a href="#orgdd52fb1">1.7. Template for text free memory</a></li>
<li><a href="#org9fb72b5">1.8. Template for has/read/write the numerical attribute</a></li>
<li><a href="#orgb34d20f">1.9. Template for has/read/write the dataset of numerical data</a></li>
<li><a href="#orgdfaab62">1.10. Template for has/read/write the dataset of strings</a></li>
<li><a href="#org8b23234">1.11. Template for has/read/write the string attribute</a></li>
<li><a href="#orgb952315">1.12. RDM struct (hard-coded)</a>
<li><a href="#org3c9afc1">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#org41373ae">1.2. Template for general structure in text back end</a></li>
<li><a href="#org7b53341">1.3. Initialize function (constant part)</a></li>
<li><a href="#org1c452b7">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#org9314366">1.5. Template for text read struct</a></li>
<li><a href="#org8cd99e5">1.6. Template for text flush struct</a></li>
<li><a href="#org17e3f74">1.7. Template for text free memory</a></li>
<li><a href="#orgb03555f">1.8. Template for has/read/write the numerical attribute</a></li>
<li><a href="#org0608f24">1.9. Template for has/read/write the dataset of numerical data</a></li>
<li><a href="#orgfe09923">1.10. Template for has/read/write the dataset of strings</a></li>
<li><a href="#org3d24397">1.11. Template for has/read/write the string attribute</a></li>
<li><a href="#org111b4b4">1.12. RDM struct (hard-coded)</a>
<ul>
<li><a href="#orgf5635d2">1.12.1. Read the complete struct</a></li>
<li><a href="#org3aa3caf">1.12.2. Flush the complete struct</a></li>
<li><a href="#org3b714a2">1.12.3. Free memory</a></li>
<li><a href="#orgac24852">1.12.4. Read/Write the one<sub>e</sub> attribute</a></li>
<li><a href="#orgc8feb61">1.12.5. Read/Write the two<sub>e</sub> attribute</a></li>
<li><a href="#orgaa20be5">1.12.1. Read the complete struct</a></li>
<li><a href="#orgf04d2d0">1.12.2. Flush the complete struct</a></li>
<li><a href="#orgffacc89">1.12.3. Free memory</a></li>
<li><a href="#org964df5f">1.12.4. Read/Write the one<sub>e</sub> attribute</a></li>
<li><a href="#orgfcf3a2a">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-orgc9c5222" class="outline-2">
<h2 id="orgc9c5222"><span class="section-number-2">1</span> TEXT back end</h2>
<div id="outline-container-org613b8a8" class="outline-2">
<h2 id="org613b8a8"><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-orgdfdd100" class="outline-3">
<h3 id="orgdfdd100"><span class="section-number-3">1.1</span> Template for group-related structures in text back end</h3>
<div id="outline-container-org3c9afc1" class="outline-3">
<h3 id="org3c9afc1"><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-orgc72bc6f" class="outline-3">
<h3 id="orgc72bc6f"><span class="section-number-3">1.2</span> Template for general structure in text back end</h3>
<div id="outline-container-org41373ae" class="outline-3">
<h3 id="org41373ae"><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-org6d3d5ff" class="outline-3">
<h3 id="org6d3d5ff"><span class="section-number-3">1.3</span> Initialize function (constant part)</h3>
<div id="outline-container-org7b53341" class="outline-3">
<h3 id="org7b53341"><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-org84327ec" class="outline-3">
<h3 id="org84327ec"><span class="section-number-3">1.4</span> Deinitialize function (templated part)</h3>
<div id="outline-container-org1c452b7" class="outline-3">
<h3 id="org1c452b7"><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-orgab721df" class="outline-3">
<h3 id="orgab721df"><span class="section-number-3">1.5</span> Template for text read struct</h3>
<div id="outline-container-org9314366" class="outline-3">
<h3 id="org9314366"><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-org1e1041a" class="outline-3">
<h3 id="org1e1041a"><span class="section-number-3">1.6</span> Template for text flush struct</h3>
<div id="outline-container-org8cd99e5" class="outline-3">
<h3 id="org8cd99e5"><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-orgdd52fb1" class="outline-3">
<h3 id="orgdd52fb1"><span class="section-number-3">1.7</span> Template for text free memory</h3>
<div id="outline-container-org17e3f74" class="outline-3">
<h3 id="org17e3f74"><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-org9fb72b5" class="outline-3">
<h3 id="org9fb72b5"><span class="section-number-3">1.8</span> Template for has/read/write the numerical attribute</h3>
<div id="outline-container-orgb03555f" class="outline-3">
<h3 id="orgb03555f"><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-orgb34d20f" class="outline-3">
<h3 id="orgb34d20f"><span class="section-number-3">1.9</span> Template for has/read/write the dataset of numerical data</h3>
<div id="outline-container-org0608f24" class="outline-3">
<h3 id="org0608f24"><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-orgdfaab62" class="outline-3">
<h3 id="orgdfaab62"><span class="section-number-3">1.10</span> Template for has/read/write the dataset of strings</h3>
<div id="outline-container-orgfe09923" class="outline-3">
<h3 id="orgfe09923"><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-org8b23234" class="outline-3">
<h3 id="org8b23234"><span class="section-number-3">1.11</span> Template for has/read/write the string attribute</h3>
<div id="outline-container-org3d24397" class="outline-3">
<h3 id="org3d24397"><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-orgb952315" class="outline-3">
<h3 id="orgb952315"><span class="section-number-3">1.12</span> RDM struct (hard-coded)</h3>
<div id="outline-container-org111b4b4" class="outline-3">
<h3 id="org111b4b4"><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-orgf5635d2" class="outline-4">
<h4 id="orgf5635d2"><span class="section-number-4">1.12.1</span> Read the complete struct</h4>
<div id="outline-container-orgaa20be5" class="outline-4">
<h4 id="orgaa20be5"><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-org3aa3caf" class="outline-4">
<h4 id="org3aa3caf"><span class="section-number-4">1.12.2</span> Flush the complete struct</h4>
<div id="outline-container-orgf04d2d0" class="outline-4">
<h4 id="orgf04d2d0"><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-org3b714a2" class="outline-4">
<h4 id="org3b714a2"><span class="section-number-4">1.12.3</span> Free memory</h4>
<div id="outline-container-orgffacc89" class="outline-4">
<h4 id="orgffacc89"><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-orgac24852" class="outline-4">
<h4 id="orgac24852"><span class="section-number-4">1.12.4</span> Read/Write the one<sub>e</sub> attribute</h4>
<div id="outline-container-org964df5f" class="outline-4">
<h4 id="org964df5f"><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-orgc8feb61" class="outline-4">
<h4 id="orgc8feb61"><span class="section-number-4">1.12.5</span> Read/Write the two<sub>e</sub> attribute</h4>
<div id="outline-container-orgfcf3a2a" class="outline-4">
<h4 id="orgfcf3a2a"><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: 2021-11-01 Mon 10:44</p>
<p class="date">Created: 2021-11-02 Tue 10:53</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

116
trex.html
View File

@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2021-11-01 Mon 10:44 -->
<!-- 2021-11-02 Tue 10:53 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREX Configuration file</title>
@ -333,33 +333,33 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org031abaa">1. Metadata (metadata group)</a></li>
<li><a href="#org2d7e918">2. Electron (electron group)</a></li>
<li><a href="#orgcf6925a">3. Nucleus (nucleus group)</a></li>
<li><a href="#org46c16a9">4. Effective core potentials (ecp group)</a>
<li><a href="#orgca804bf">1. Metadata (metadata group)</a></li>
<li><a href="#orga8e1199">2. Electron (electron group)</a></li>
<li><a href="#org8b0d952">3. Nucleus (nucleus group)</a></li>
<li><a href="#org0de8c4f">4. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org28787b4">4.1. Example</a></li>
<li><a href="#org2621430">4.1. Example</a></li>
</ul>
</li>
<li><a href="#org9591dd0">5. Basis set (basis group)</a>
<li><a href="#org4a099af">5. Basis set (basis group)</a>
<ul>
<li><a href="#org26ef5d4">5.1. Example</a></li>
<li><a href="#org9cc161f">5.1. Example</a></li>
</ul>
</li>
<li><a href="#org79d80ed">6. Atomic orbitals (ao group)</a>
<li><a href="#org08d1365">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="#orge6190cb">7. Molecular orbitals (mo group)</a>
<li><a href="#orgda8323e">7. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#orgcf17b8c">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orge39c941">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org9352125">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgdaf8a6f">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#org12cadb2">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#org5fc3ee3">9. <span class="todo TODO">TODO</span> Reduced density matrices (rdm group)</a></li>
<li><a href="#org4ae0348">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#orgfdbd80e">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-org031abaa" class="outline-2">
<h2 id="org031abaa"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-orgca804bf" class="outline-2">
<h2 id="orgca804bf"><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="org530de12" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org1bb61be" 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-org2d7e918" class="outline-2">
<h2 id="org2d7e918"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div id="outline-container-orga8e1199" class="outline-2">
<h2 id="orga8e1199"><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="org8db50c0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org532b4a9" 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-orgcf6925a" class="outline-2">
<h2 id="orgcf6925a"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div id="outline-container-org8b0d952" class="outline-2">
<h2 id="org8b0d952"><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="orgb85e6a2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgfe034da" 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-org46c16a9" class="outline-2">
<h2 id="org46c16a9"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div id="outline-container-org0de8c4f" class="outline-2">
<h2 id="org0de8c4f"><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="org34358c3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org7e4b62f" 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-org28787b4" class="outline-3">
<h3 id="org28787b4"><span class="section-number-3">4.1</span> Example</h3>
<div id="outline-container-org2621430" class="outline-3">
<h3 id="org2621430"><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-org9591dd0" class="outline-2">
<h2 id="org9591dd0"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div id="outline-container-org4a099af" class="outline-2">
<h2 id="org4a099af"><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="org8f257c0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc599a61" 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-org26ef5d4" class="outline-3">
<h3 id="org26ef5d4"><span class="section-number-3">5.1</span> Example</h3>
<div id="outline-container-org9cc161f" class="outline-3">
<h3 id="org9cc161f"><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-org79d80ed" class="outline-2">
<h2 id="org79d80ed"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div id="outline-container-org08d1365" class="outline-2">
<h2 id="org08d1365"><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="#org9591dd0">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#org4a099af">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="org9f58294" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org09ff5a2" 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-org3a74f69" class="outline-3">
<h3 id="ao_one_e"><a id="org3a74f69"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div id="outline-container-orgb10e3e0" class="outline-3">
<h3 id="ao_one_e"><a id="orgb10e3e0"></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="orgf710f0f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd2d6f24" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1208,8 +1208,8 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-orgd7110a7" class="outline-3">
<h3 id="ao_two_e"><a id="orgd7110a7"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div id="outline-container-org1092df1" class="outline-3">
<h3 id="ao_two_e"><a id="org1092df1"></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="org68b9375" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf74bcb5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1270,10 +1270,10 @@ notation.
</div>
</div>
<div id="outline-container-orge6190cb" class="outline-2">
<h2 id="orge6190cb"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div id="outline-container-orgda8323e" class="outline-2">
<h2 id="orgda8323e"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div class="outline-text-2" id="text-7">
<table id="org63e3d18" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga859a7a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1339,8 +1339,8 @@ notation.
</table>
</div>
<div id="outline-container-orgcf17b8c" class="outline-3">
<h3 id="orgcf17b8c"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div id="outline-container-org9352125" class="outline-3">
<h3 id="org9352125"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div class="outline-text-3" id="text-7-1">
<p>
The operators as the same as those defined in the
@ -1348,7 +1348,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org0fc34bf" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org7abcd4c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1415,8 +1415,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-orge39c941" class="outline-3">
<h3 id="orge39c941"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div id="outline-container-orgdaf8a6f" class="outline-3">
<h3 id="orgdaf8a6f"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div class="outline-text-3" id="text-7-2">
<p>
The operators as the same as those defined in the
@ -1424,7 +1424,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org3fb3ae2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgde66d24" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1464,13 +1464,13 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org12cadb2" class="outline-2">
<h2 id="org12cadb2"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
<div id="outline-container-org4ae0348" class="outline-2">
<h2 id="org4ae0348"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
</div>
<div id="outline-container-org5fc3ee3" class="outline-2">
<h2 id="org5fc3ee3"><span class="section-number-2">9</span> <span class="todo TODO">TODO</span> Reduced density matrices (rdm group)</h2>
<div id="outline-container-orgfdbd80e" class="outline-2">
<h2 id="orgfdbd80e"><span class="section-number-2">9</span> <span class="todo TODO">TODO</span> Reduced density matrices (rdm group)</h2>
<div class="outline-text-2" id="text-9">
<table id="org3337c77" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org4e9cabc" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1525,7 +1525,7 @@ the basis of molecular orbitals.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2021-11-01 Mon 10:44</p>
<p class="date">Created: 2021-11-02 Tue 10:53</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>