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This commit is contained in:
scemama
parent
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commit
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@ -3,7 +3,7 @@
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
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||||
<head>
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<!-- 2021-06-22 Tue 10:22 -->
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<!-- 2021-06-22 Tue 20:32 -->
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
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<meta name="viewport" content="width=device-width, initial-scale=1" />
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<title>TREXIO source code documentation</title>
|
||||
@ -342,7 +342,7 @@ and bug reports should be submitted at
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2021-06-22 Tue 10:22</p>
|
||||
<p class="date">Created: 2021-06-22 Tue 20:32</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
16
Sparse.html
16
Sparse.html
@ -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>
|
||||
<!-- 2021-06-22 Tue 10:22 -->
|
||||
<!-- 2021-06-22 Tue 20:32 -->
|
||||
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
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<meta name="viewport" content="width=device-width, initial-scale=1" />
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<title>‎</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="#org72f5cf5">1. Text back end</a></li>
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<li><a href="#org055c88d">2. HDF5 Back end</a></li>
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<li><a href="#org669d292">1. Text back end</a></li>
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<li><a href="#org6e3b15f">2. HDF5 Back end</a></li>
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</ul>
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||||
</div>
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</div>
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@ -241,8 +241,8 @@ for the JavaScript code in this tag.
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See templator<sub>front.org</sub>
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</p>
|
||||
|
||||
<div id="outline-container-org72f5cf5" class="outline-2">
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<h2 id="org72f5cf5"><span class="section-number-2">1</span> Text back end</h2>
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||||
<div id="outline-container-org669d292" class="outline-2">
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<h2 id="org669d292"><span class="section-number-2">1</span> Text back end</h2>
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<div class="outline-text-2" id="text-1">
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<p>
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As the size of the dataset should be extensible, the simplest
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@ -256,8 +256,8 @@ The offset can be used with <code>fseek(69L*offset, SEEK_SET)</code>
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</div>
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</div>
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<div id="outline-container-org055c88d" class="outline-2">
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<h2 id="org055c88d"><span class="section-number-2">2</span> HDF5 Back end</h2>
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<div id="outline-container-org6e3b15f" class="outline-2">
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<h2 id="org6e3b15f"><span class="section-number-2">2</span> HDF5 Back end</h2>
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<div class="outline-text-2" id="text-2">
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<p>
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We need to declare the number of rows of the dataset as
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@ -278,7 +278,7 @@ If the offset+num > nmax, we need to extend the dataset.
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</div>
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</div>
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||||
<div id="postamble" class="status">
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<p class="date">Created: 2021-06-22 Tue 10:22</p>
|
||||
<p class="date">Created: 2021-06-22 Tue 20:32</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
@ -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>
|
||||
<!-- 2021-06-22 Tue 10:22 -->
|
||||
<!-- 2021-06-22 Tue 20:32 -->
|
||||
<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>
|
||||
@ -342,7 +342,7 @@ and bug reports should be submitted at
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2021-06-22 Tue 10:22</p>
|
||||
<p class="date">Created: 2021-06-22 Tue 20:32</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
@ -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>
|
||||
<!-- 2021-06-22 Tue 10:22 -->
|
||||
<!-- 2021-06-22 Tue 20:32 -->
|
||||
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
|
||||
<meta name="viewport" content="width=device-width, initial-scale=1" />
|
||||
<title>Front end API</title>
|
||||
@ -333,61 +333,61 @@ for the JavaScript code in this tag.
|
||||
<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
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||||
<li><a href="#org825a5a0">1. Coding conventions</a>
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<li><a href="#org8666d98">1. Coding conventions</a>
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<ul>
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<li><a href="#orge2f8a55">1.1. Memory allocation</a></li>
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<li><a href="#orge6c2bb4">1.1. Memory allocation</a></li>
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</ul>
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</li>
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<li><a href="#org96fc97d">2. Front end</a>
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<li><a href="#org9257f5e">2. Front end</a>
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<ul>
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<li><a href="#orgc0d8632">2.1. Error handling</a></li>
|
||||
<li><a href="#org0aa5079">2.2. Back ends</a></li>
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<li><a href="#org8c7226e">2.3. Read/write behavior</a></li>
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<li><a href="#orga195db7">2.4. TREXIO file type</a></li>
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<li><a href="#orgf2c3ab7">2.5. Polymorphism of the file handle</a></li>
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||||
<li><a href="#org73bd8f3">2.6. File opening</a></li>
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<li><a href="#orgd6e06c9">2.7. File closing</a></li>
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||||
<li><a href="#org4fbe34f">2.1. Error handling</a></li>
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<li><a href="#org93f2d92">2.2. Back ends</a></li>
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<li><a href="#org771d809">2.3. Read/write behavior</a></li>
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<li><a href="#orgc16ca33">2.4. TREXIO file type</a></li>
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<li><a href="#org00a6f6c">2.5. Polymorphism of the file handle</a></li>
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||||
<li><a href="#org4a11d39">2.6. File opening</a></li>
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||||
<li><a href="#org7fa48e9">2.7. File closing</a></li>
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</ul>
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||||
</li>
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||||
<li><a href="#orgdf1e9c4">3. Templates for front end</a>
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<li><a href="#org9e9ceb0">3. Templates for front end</a>
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||||
<ul>
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||||
<li><a href="#orgaec4c11">3.1. Description</a></li>
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||||
<li><a href="#orgdb20b39">3.2. Templates for front end has/read/write a single dimensioning variable</a>
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||||
<li><a href="#orgb355e46">3.1. Description</a></li>
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||||
<li><a href="#org1e00480">3.2. Templates for front end has/read/write a single dimensioning variable</a>
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||||
<ul>
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<li><a href="#orgb169558">3.2.1. C templates for front end</a></li>
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<li><a href="#org5e69b90">3.2.2. Fortran templates for front end</a></li>
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||||
<li><a href="#orgfb31c9c">3.2.1. C templates for front end</a></li>
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<li><a href="#orgb372859">3.2.2. Fortran templates for front end</a></li>
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||||
</ul>
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||||
</li>
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||||
<li><a href="#org5d80755">3.3. Templates for front end has/read/write a dataset of numerical data</a>
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<li><a href="#orgde36d9e">3.3. Templates for front end has/read/write a dataset of numerical data</a>
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||||
<ul>
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<li><a href="#org16585b5">3.3.1. C templates for front end</a></li>
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||||
<li><a href="#orge4a641e">3.3.2. Fortran templates for front end</a></li>
|
||||
<li><a href="#org58f704b">3.3.1. C templates for front end</a></li>
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||||
<li><a href="#org454e011">3.3.2. Fortran templates for front end</a></li>
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||||
</ul>
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||||
</li>
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||||
<li><a href="#orgf888836">3.4. Sparse data structures</a></li>
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||||
<li><a href="#org93f30b9">3.5. Templates for front end has/read/write a dataset of strings</a>
|
||||
<li><a href="#orga3691f4">3.4. Sparse data structures</a></li>
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||||
<li><a href="#orgabdfca4">3.5. Templates for front end has/read/write a dataset of strings</a>
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||||
<ul>
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||||
<li><a href="#orgba96594">3.5.1. Introduction</a></li>
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<li><a href="#orgfa762ea">3.5.2. C templates for front end</a></li>
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<li><a href="#org2346c52">3.5.3. Fortran templates for front end</a></li>
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||||
<li><a href="#org88aadc3">3.5.1. Introduction</a></li>
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||||
<li><a href="#orga58341a">3.5.2. C templates for front end</a></li>
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||||
<li><a href="#org0210dc2">3.5.3. Fortran templates for front end</a></li>
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||||
</ul>
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</li>
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||||
<li><a href="#orgb7b49c5">3.6. Templates for front end has/read/write a single string attribute</a>
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||||
<li><a href="#org1113730">3.6. Templates for front end has/read/write a single string attribute</a>
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||||
<ul>
|
||||
<li><a href="#org98b2793">3.6.1. Introduction</a></li>
|
||||
<li><a href="#orgab59381">3.6.2. C templates for front end</a></li>
|
||||
<li><a href="#orgf778bf1">3.6.3. Fortran templates for front end</a></li>
|
||||
<li><a href="#org00c55c0">3.6.1. Introduction</a></li>
|
||||
<li><a href="#orgb00afa8">3.6.2. C templates for front end</a></li>
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||||
<li><a href="#org6cf2f25">3.6.3. Fortran templates for front end</a></li>
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</ul>
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</li>
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</ul>
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</li>
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||||
<li><a href="#orge3060b4">4. Fortran helper/wrapper functions</a></li>
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||||
<li><a href="#org945ebd6">4. Fortran helper/wrapper functions</a></li>
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||||
</ul>
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||||
</div>
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</div>
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||||
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||||
<div id="outline-container-org825a5a0" class="outline-2">
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<h2 id="org825a5a0"><span class="section-number-2">1</span> Coding conventions</h2>
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<div id="outline-container-org8666d98" class="outline-2">
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||||
<h2 id="org8666d98"><span class="section-number-2">1</span> Coding conventions</h2>
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<div class="outline-text-2" id="text-1">
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<ul class="org-ul">
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<li>integer types will be defined using types given in <code>stdint.h</code></li>
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@ -402,8 +402,8 @@ for the JavaScript code in this tag.
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</ul>
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</div>
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<div id="outline-container-orge2f8a55" class="outline-3">
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||||
<h3 id="orge2f8a55"><span class="section-number-3">1.1</span> Memory allocation</h3>
|
||||
<div id="outline-container-orge6c2bb4" class="outline-3">
|
||||
<h3 id="orge6c2bb4"><span class="section-number-3">1.1</span> Memory allocation</h3>
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<div class="outline-text-3" id="text-1-1">
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<p>
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Memory allocation of structures can be facilitated by using the
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@ -438,8 +438,8 @@ The maximum string size for the filenames is 4096 characters.
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</div>
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</div>
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<div id="outline-container-org96fc97d" class="outline-2">
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<h2 id="org96fc97d"><span class="section-number-2">2</span> Front end</h2>
|
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<div id="outline-container-org9257f5e" class="outline-2">
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||||
<h2 id="org9257f5e"><span class="section-number-2">2</span> Front end</h2>
|
||||
<div class="outline-text-2" id="text-2">
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||||
<p>
|
||||
All calls to TREXIO are thread-safe.
|
||||
@ -447,10 +447,10 @@ TREXIO front end is modular, which simplifies implementation of new back ends.
|
||||
</p>
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||||
</div>
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||||
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||||
<div id="outline-container-orgc0d8632" class="outline-3">
|
||||
<h3 id="orgc0d8632"><span class="section-number-3">2.1</span> Error handling</h3>
|
||||
<div id="outline-container-org4fbe34f" class="outline-3">
|
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<h3 id="org4fbe34f"><span class="section-number-3">2.1</span> Error handling</h3>
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<div class="outline-text-3" id="text-2-1">
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<table id="org1997f08" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
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||||
<table id="orgf5c43a6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
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<colgroup>
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@ -553,9 +553,9 @@ TREXIO front end is modular, which simplifies implementation of new back ends.
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</tr>
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<tr>
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<td class="org-left"><code>TREXIO_NUM_ALREADY_EXISTS</code></td>
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<td class="org-left"><code>TREXIO_ATTR_ALREADY_EXISTS</code></td>
|
||||
<td class="org-right">13</td>
|
||||
<td class="org-left">'Dimensioning variable already exists'</td>
|
||||
<td class="org-left">'Attribute (num/str) already exists'</td>
|
||||
</tr>
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<tr>
|
||||
@ -691,8 +691,8 @@ The text strings are extracted from the previous table.
|
||||
<span style="color: #a020f0;">case</span> TREXIO_INVALID_NUM:
|
||||
<span style="color: #a020f0;">return</span> <span style="color: #8b2252;">"Invalid dimensions"</span>;
|
||||
<span style="color: #a020f0;">break</span>;
|
||||
<span style="color: #a020f0;">case</span> TREXIO_NUM_ALREADY_EXISTS:
|
||||
<span style="color: #a020f0;">return</span> <span style="color: #8b2252;">"Dimensioning variable already exists"</span>;
|
||||
<span style="color: #a020f0;">case</span> TREXIO_ATTR_ALREADY_EXISTS:
|
||||
<span style="color: #a020f0;">return</span> <span style="color: #8b2252;">"Attribute (num/str) already exists"</span>;
|
||||
<span style="color: #a020f0;">break</span>;
|
||||
<span style="color: #a020f0;">case</span> TREXIO_DSET_ALREADY_EXISTS:
|
||||
<span style="color: #a020f0;">return</span> <span style="color: #8b2252;">"Dataset already exists"</span>;
|
||||
@ -750,8 +750,8 @@ The text strings are extracted from the previous table.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org0aa5079" class="outline-3">
|
||||
<h3 id="org0aa5079"><span class="section-number-3">2.2</span> Back ends</h3>
|
||||
<div id="outline-container-org93f2d92" class="outline-3">
|
||||
<h3 id="org93f2d92"><span class="section-number-3">2.2</span> Back ends</h3>
|
||||
<div class="outline-text-3" id="text-2-2">
|
||||
<p>
|
||||
TREXIO has several back ends:
|
||||
@ -783,8 +783,8 @@ lines that correspond to the <code>TREXIO_JSON</code> back end (not implemented
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-org8c7226e" class="outline-3">
|
||||
<h3 id="org8c7226e"><span class="section-number-3">2.3</span> Read/write behavior</h3>
|
||||
<div id="outline-container-org771d809" class="outline-3">
|
||||
<h3 id="org771d809"><span class="section-number-3">2.3</span> Read/write behavior</h3>
|
||||
<div class="outline-text-3" id="text-2-3">
|
||||
<p>
|
||||
Every time a reading function is called, the data is read from the
|
||||
@ -812,8 +812,8 @@ concurrent programs, the behavior is not specified.
|
||||
</p>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-orga195db7" class="outline-3">
|
||||
<h3 id="orga195db7"><span class="section-number-3">2.4</span> TREXIO file type</h3>
|
||||
<div id="outline-container-orgc16ca33" class="outline-3">
|
||||
<h3 id="orgc16ca33"><span class="section-number-3">2.4</span> TREXIO file type</h3>
|
||||
<div class="outline-text-3" id="text-2-4">
|
||||
<p>
|
||||
<code>trexio_s</code> is the the main type for TREXIO files, visible to the users
|
||||
@ -846,8 +846,8 @@ TREXIO files will have as a first argument the TREXIO file handle.
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-orgf2c3ab7" class="outline-3">
|
||||
<h3 id="orgf2c3ab7"><span class="section-number-3">2.5</span> Polymorphism of the file handle</h3>
|
||||
<div id="outline-container-org00a6f6c" class="outline-3">
|
||||
<h3 id="org00a6f6c"><span class="section-number-3">2.5</span> Polymorphism of the file handle</h3>
|
||||
<div class="outline-text-3" id="text-2-5">
|
||||
<p>
|
||||
Polymorphism of the <code>trexio_t</code> type is handled by ensuring that the
|
||||
@ -866,8 +866,8 @@ corresponding types for all back ends can be safely casted to
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org73bd8f3" class="outline-3">
|
||||
<h3 id="org73bd8f3"><span class="section-number-3">2.6</span> File opening</h3>
|
||||
<div id="outline-container-org4a11d39" class="outline-3">
|
||||
<h3 id="org4a11d39"><span class="section-number-3">2.6</span> File opening</h3>
|
||||
<div class="outline-text-3" id="text-2-6">
|
||||
<p>
|
||||
<code>trexio_open</code> creates a new TREXIO file or opens existing one.
|
||||
@ -1058,8 +1058,8 @@ know if we need to shift by 1 arrays of indices.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgd6e06c9" class="outline-3">
|
||||
<h3 id="orgd6e06c9"><span class="section-number-3">2.7</span> File closing</h3>
|
||||
<div id="outline-container-org7fa48e9" class="outline-3">
|
||||
<h3 id="org7fa48e9"><span class="section-number-3">2.7</span> File closing</h3>
|
||||
<div class="outline-text-3" id="text-2-7">
|
||||
<p>
|
||||
<code>trexio_close</code> closes an existing <code>trexio_t</code> file.
|
||||
@ -1155,12 +1155,12 @@ output:
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgdf1e9c4" class="outline-2">
|
||||
<h2 id="orgdf1e9c4"><span class="section-number-2">3</span> Templates for front end</h2>
|
||||
<div id="outline-container-org9e9ceb0" class="outline-2">
|
||||
<h2 id="org9e9ceb0"><span class="section-number-2">3</span> Templates for front end</h2>
|
||||
<div class="outline-text-2" id="text-3">
|
||||
</div>
|
||||
<div id="outline-container-orgaec4c11" class="outline-3">
|
||||
<h3 id="orgaec4c11"><span class="section-number-3">3.1</span> Description</h3>
|
||||
<div id="outline-container-orgb355e46" class="outline-3">
|
||||
<h3 id="orgb355e46"><span class="section-number-3">3.1</span> Description</h3>
|
||||
<div class="outline-text-3" id="text-3-1">
|
||||
<p>
|
||||
Consider the following block of <code>trex.json</code>:
|
||||
@ -1350,8 +1350,8 @@ or double precision for integer and floating point numbers.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgdb20b39" class="outline-3">
|
||||
<h3 id="orgdb20b39"><span class="section-number-3">3.2</span> Templates for front end has/read/write a single dimensioning variable</h3>
|
||||
<div id="outline-container-org1e00480" class="outline-3">
|
||||
<h3 id="org1e00480"><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">
|
||||
<p>
|
||||
This section concerns API calls related to dimensioning variables.
|
||||
@ -1420,8 +1420,8 @@ This section concerns API calls related to dimensioning variables.
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgb169558" class="outline-4">
|
||||
<h4 id="orgb169558"><span class="section-number-4">3.2.1</span> C templates for front end</h4>
|
||||
<div id="outline-container-orgfb31c9c" class="outline-4">
|
||||
<h4 id="orgfb31c9c"><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">
|
||||
<p>
|
||||
The <code>C</code> templates that correspond to each of the abovementioned
|
||||
@ -1474,7 +1474,7 @@ precision (see Table above).
|
||||
{
|
||||
<span style="color: #a020f0;">if</span> (file == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_1;
|
||||
<span style="color: #a020f0;">if</span> (num < 0 ) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_2;
|
||||
<span style="color: #a020f0;">if</span> (trexio_has_$group_num$(file) == TREXIO_SUCCESS) <span style="color: #a020f0;">return</span> TREXIO_NUM_ALREADY_EXISTS;
|
||||
<span style="color: #a020f0;">if</span> (trexio_has_$group_num$(file) == TREXIO_SUCCESS) <span style="color: #a020f0;">return</span> TREXIO_ATTR_ALREADY_EXISTS;
|
||||
|
||||
<span style="color: #a020f0;">switch</span> (file->back_end) {
|
||||
|
||||
@ -1537,7 +1537,7 @@ precision (see Table above).
|
||||
|
||||
<span style="color: #a020f0;">if</span> (file == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_1;
|
||||
<span style="color: #a020f0;">if</span> (num < 0 ) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_2;
|
||||
<span style="color: #a020f0;">if</span> (trexio_has_$group_num$(file) == TREXIO_SUCCESS) <span style="color: #a020f0;">return</span> TREXIO_NUM_ALREADY_EXISTS;
|
||||
<span style="color: #a020f0;">if</span> (trexio_has_$group_num$(file) == TREXIO_SUCCESS) <span style="color: #a020f0;">return</span> TREXIO_ATTR_ALREADY_EXISTS;
|
||||
|
||||
<span style="color: #a020f0;">switch</span> (file->back_end) {
|
||||
|
||||
@ -1610,8 +1610,8 @@ precision (see Table above).
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org5e69b90" class="outline-4">
|
||||
<h4 id="org5e69b90"><span class="section-number-4">3.2.2</span> Fortran templates for front end</h4>
|
||||
<div id="outline-container-orgb372859" class="outline-4">
|
||||
<h4 id="orgb372859"><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">
|
||||
<p>
|
||||
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 id="outline-container-org5d80755" class="outline-3">
|
||||
<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 id="outline-container-orgde36d9e" class="outline-3">
|
||||
<h3 id="orgde36d9e"><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">
|
||||
<p>
|
||||
This section concerns API calls related to datasets.
|
||||
@ -1767,8 +1767,8 @@ This section concerns API calls related to datasets.
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org16585b5" class="outline-4">
|
||||
<h4 id="org16585b5"><span class="section-number-4">3.3.1</span> C templates for front end</h4>
|
||||
<div id="outline-container-org58f704b" class="outline-4">
|
||||
<h4 id="org58f704b"><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">
|
||||
<p>
|
||||
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 id="outline-container-orge4a641e" class="outline-4">
|
||||
<h4 id="orge4a641e"><span class="section-number-4">3.3.2</span> Fortran templates for front end</h4>
|
||||
<div id="outline-container-org454e011" class="outline-4">
|
||||
<h4 id="org454e011"><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">
|
||||
<p>
|
||||
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 id="outline-container-orgf888836" class="outline-3">
|
||||
<h3 id="orgf888836"><span class="section-number-3">3.4</span> Sparse data structures</h3>
|
||||
<div id="outline-container-orga3691f4" class="outline-3">
|
||||
<h3 id="orga3691f4"><span class="section-number-3">3.4</span> Sparse data structures</h3>
|
||||
<div class="outline-text-3" id="text-3-4">
|
||||
<p>
|
||||
Sparse data structures are used typically for large tensors such as
|
||||
@ -2316,12 +2316,12 @@ For the values,
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org93f30b9" class="outline-3">
|
||||
<h3 id="org93f30b9"><span class="section-number-3">3.5</span> Templates for front end has/read/write a dataset of strings</h3>
|
||||
<div id="outline-container-orgabdfca4" class="outline-3">
|
||||
<h3 id="orgabdfca4"><span class="section-number-3">3.5</span> Templates for front end has/read/write a dataset of strings</h3>
|
||||
<div class="outline-text-3" id="text-3-5">
|
||||
</div>
|
||||
<div id="outline-container-orgba96594" class="outline-4">
|
||||
<h4 id="orgba96594"><span class="section-number-4">3.5.1</span> Introduction</h4>
|
||||
<div id="outline-container-org88aadc3" class="outline-4">
|
||||
<h4 id="org88aadc3"><span class="section-number-4">3.5.1</span> Introduction</h4>
|
||||
<div class="outline-text-4" id="text-3-5-1">
|
||||
<p>
|
||||
This section concerns API calls related to datasets of strings.
|
||||
@ -2361,8 +2361,8 @@ This section concerns API calls related to datasets of strings.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgfa762ea" class="outline-4">
|
||||
<h4 id="orgfa762ea"><span class="section-number-4">3.5.2</span> C templates for front end</h4>
|
||||
<div id="outline-container-orga58341a" class="outline-4">
|
||||
<h4 id="orga58341a"><span class="section-number-4">3.5.2</span> C templates for front end</h4>
|
||||
<div class="outline-text-4" id="text-3-5-2">
|
||||
<p>
|
||||
First parameter is the <code>TREXIO</code> file handle. Second parameter is the variable to be written/read
|
||||
@ -2605,8 +2605,8 @@ to/from the <code>TREXIO</code> file (except for <code>trexio_has_</code> functi
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org2346c52" class="outline-4">
|
||||
<h4 id="org2346c52"><span class="section-number-4">3.5.3</span> Fortran templates for front end</h4>
|
||||
<div id="outline-container-org0210dc2" class="outline-4">
|
||||
<h4 id="org0210dc2"><span class="section-number-4">3.5.3</span> Fortran templates for front end</h4>
|
||||
<div class="outline-text-4" id="text-3-5-3">
|
||||
<p>
|
||||
The <code>Fortran</code> templates that provide an access to the <code>C</code> API calls from <code>Fortran</code>.
|
||||
@ -2703,12 +2703,12 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgb7b49c5" class="outline-3">
|
||||
<h3 id="orgb7b49c5"><span class="section-number-3">3.6</span> Templates for front end has/read/write a single string attribute</h3>
|
||||
<div id="outline-container-org1113730" class="outline-3">
|
||||
<h3 id="org1113730"><span class="section-number-3">3.6</span> Templates for front end has/read/write a single string attribute</h3>
|
||||
<div class="outline-text-3" id="text-3-6">
|
||||
</div>
|
||||
<div id="outline-container-org98b2793" class="outline-4">
|
||||
<h4 id="org98b2793"><span class="section-number-4">3.6.1</span> Introduction</h4>
|
||||
<div id="outline-container-org00c55c0" class="outline-4">
|
||||
<h4 id="org00c55c0"><span class="section-number-4">3.6.1</span> Introduction</h4>
|
||||
<div class="outline-text-4" id="text-3-6-1">
|
||||
<p>
|
||||
This section concerns API calls related to string attributes.
|
||||
@ -2748,8 +2748,8 @@ This section concerns API calls related to string attributes.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgab59381" class="outline-4">
|
||||
<h4 id="orgab59381"><span class="section-number-4">3.6.2</span> C templates for front end</h4>
|
||||
<div id="outline-container-orgb00afa8" class="outline-4">
|
||||
<h4 id="orgb00afa8"><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="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -2791,7 +2791,7 @@ This section concerns API calls related to string attributes.
|
||||
<span style="color: #a020f0;">if</span> (file == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_1;
|
||||
<span style="color: #a020f0;">if</span> (str == <span style="color: #008b8b;">NULL</span>) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_2;
|
||||
<span style="color: #a020f0;">if</span> (max_str_len <= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ARG_3;
|
||||
<span style="color: #a020f0;">if</span> (trexio_has_$group_str$(file) == TREXIO_SUCCESS) <span style="color: #a020f0;">return</span> TREXIO_NUM_ALREADY_EXISTS;
|
||||
<span style="color: #a020f0;">if</span> (trexio_has_$group_str$(file) == TREXIO_SUCCESS) <span style="color: #a020f0;">return</span> TREXIO_ATTR_ALREADY_EXISTS;
|
||||
|
||||
<span style="color: #228b22;">size_t</span> <span style="color: #a0522d;">len_write</span> = strlen(str);
|
||||
<span style="color: #a020f0;">if</span> (max_str_len < len_write) <span style="color: #a020f0;">return</span> TREXIO_INVALID_STR_LEN;
|
||||
@ -2849,8 +2849,8 @@ This section concerns API calls related to string attributes.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgf778bf1" class="outline-4">
|
||||
<h4 id="orgf778bf1"><span class="section-number-4">3.6.3</span> Fortran templates for front end</h4>
|
||||
<div id="outline-container-org6cf2f25" class="outline-4">
|
||||
<h4 id="org6cf2f25"><span class="section-number-4">3.6.3</span> Fortran templates for front end</h4>
|
||||
<div class="outline-text-4" id="text-3-6-3">
|
||||
<p>
|
||||
The <code>Fortran</code> templates that provide an access to the <code>C</code> API calls from Fortran.
|
||||
@ -2929,8 +2929,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orge3060b4" class="outline-2">
|
||||
<h2 id="orge3060b4"><span class="section-number-2">4</span> Fortran helper/wrapper functions</h2>
|
||||
<div id="outline-container-org945ebd6" class="outline-2">
|
||||
<h2 id="org945ebd6"><span class="section-number-2">4</span> Fortran helper/wrapper functions</h2>
|
||||
<div class="outline-text-2" id="text-4">
|
||||
<p>
|
||||
The function below adapts the original C-based <code>trexio_open</code> for Fortran.
|
||||
@ -3064,7 +3064,7 @@ two code are identical, i.e. if the <code>assert</code> statement pass.
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2021-06-22 Tue 10:22</p>
|
||||
<p class="date">Created: 2021-06-22 Tue 20:32</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
@ -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>
|
||||
<!-- 2021-06-22 Tue 10:22 -->
|
||||
<!-- 2021-06-22 Tue 20:32 -->
|
||||
<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="#orgc3d3253">1. HDF5 back end</a>
|
||||
<li><a href="#orgaed42d9">1. HDF5 back end</a>
|
||||
<ul>
|
||||
<li><a href="#orgdb2e5c8">1.1. Template for HDF5 definitions</a></li>
|
||||
<li><a href="#org47561d9">1.2. Template for HDF5 structures</a></li>
|
||||
<li><a href="#org4835c4a">1.3. Template for HDF5 init/deinit</a></li>
|
||||
<li><a href="#org345f4c1">1.4. Template for HDF5 has/read/write a single dimensioning variable</a></li>
|
||||
<li><a href="#orgfbe4bec">1.5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#org4197b20">1.6. Template for HDF5 has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#org2d1e0a9">1.7. Template for HDF5 has/read/write a single string attribute</a></li>
|
||||
<li><a href="#orga63cd3e">1.1. Template for HDF5 definitions</a></li>
|
||||
<li><a href="#org77867da">1.2. Template for HDF5 structures</a></li>
|
||||
<li><a href="#org595f8f6">1.3. Template for HDF5 init/deinit</a></li>
|
||||
<li><a href="#org158ffac">1.4. Template for HDF5 has/read/write a single dimensioning variable</a></li>
|
||||
<li><a href="#orga702a5a">1.5. Template for HDF5 has/read/write a dataset of numerical data</a></li>
|
||||
<li><a href="#org45c67c1">1.6. Template for HDF5 has/read/write a dataset of strings</a></li>
|
||||
<li><a href="#orgd1d2c79">1.7. Template for HDF5 has/read/write a single string attribute</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgc3d3253" class="outline-2">
|
||||
<h2 id="orgc3d3253"><span class="section-number-2">1</span> HDF5 back end</h2>
|
||||
<div id="outline-container-orgaed42d9" class="outline-2">
|
||||
<h2 id="orgaed42d9"><span class="section-number-2">1</span> HDF5 back end</h2>
|
||||
<div class="outline-text-2" id="text-1">
|
||||
</div>
|
||||
<div id="outline-container-orgdb2e5c8" class="outline-3">
|
||||
<h3 id="orgdb2e5c8"><span class="section-number-3">1.1</span> Template for HDF5 definitions</h3>
|
||||
<div id="outline-container-orga63cd3e" class="outline-3">
|
||||
<h3 id="orga63cd3e"><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-org47561d9" class="outline-3">
|
||||
<h3 id="org47561d9"><span class="section-number-3">1.2</span> Template for HDF5 structures</h3>
|
||||
<div id="outline-container-org77867da" class="outline-3">
|
||||
<h3 id="org77867da"><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> {
|
||||
@ -359,8 +359,8 @@ for the JavaScript code in this tag.
|
||||
</div>
|
||||
|
||||
|
||||
<div id="outline-container-org4835c4a" class="outline-3">
|
||||
<h3 id="org4835c4a"><span class="section-number-3">1.3</span> Template for HDF5 init/deinit</h3>
|
||||
<div id="outline-container-org595f8f6" class="outline-3">
|
||||
<h3 id="org595f8f6"><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>
|
||||
@ -440,8 +440,8 @@ for the JavaScript code in this tag.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org345f4c1" class="outline-3">
|
||||
<h3 id="org345f4c1"><span class="section-number-3">1.4</span> Template for HDF5 has/read/write a single dimensioning variable</h3>
|
||||
<div id="outline-container-org158ffac" class="outline-3">
|
||||
<h3 id="org158ffac"><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="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -515,25 +515,16 @@ for the JavaScript code in this tag.
|
||||
<span style="color: #228b22;">trexio_exit_code</span> <span style="color: #a0522d;">rc</span> = trexio_hdf5_read_$group_num$(file, &(infile_num));
|
||||
<span style="color: #a020f0;">if</span> (rc != TREXIO_SUCCESS) <span style="color: #a020f0;">return</span> rc;
|
||||
|
||||
<span style="color: #a020f0;">if</span> (infile_num != num) {
|
||||
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dtype</span> = H5Tcopy(H5T_NATIVE_UINT64);
|
||||
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">num_id</span> = H5Aopen(f->$group$_group, $GROUP_NUM$_NAME, H5P_DEFAULT);
|
||||
<span style="color: #a020f0;">if</span> (num_id <= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
|
||||
|
||||
<span style="color: #a020f0;">if</span> (infile_num != 0) {
|
||||
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5Awrite(num_id, dtype, &(num));
|
||||
<span style="color: #a020f0;">if</span> (status < 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
|
||||
|
||||
<span style="color: #a020f0;">return</span> TREXIO_NUM_ALREADY_EXISTS;
|
||||
H5Aclose(num_id);
|
||||
H5Tclose(dtype);
|
||||
|
||||
} <span style="color: #a020f0;">else</span> {
|
||||
|
||||
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">dtype</span> = H5Tcopy(H5T_NATIVE_UINT64);
|
||||
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">hid_t</span> <span style="color: #a0522d;">num_id</span> = H5Aopen(f->$group$_group, $GROUP_NUM$_NAME, H5P_DEFAULT);
|
||||
<span style="color: #a020f0;">if</span> (num_id <= 0) <span style="color: #a020f0;">return</span> TREXIO_INVALID_ID;
|
||||
|
||||
<span style="color: #a020f0;">const</span> <span style="color: #228b22;">herr_t</span> <span style="color: #a0522d;">status</span> = H5Awrite(num_id, dtype, &(num));
|
||||
<span style="color: #a020f0;">if</span> (status < 0) <span style="color: #a020f0;">return</span> TREXIO_FAILURE;
|
||||
|
||||
H5Aclose(num_id);
|
||||
H5Tclose(dtype);
|
||||
}
|
||||
}
|
||||
<span style="color: #a020f0;">return</span> TREXIO_SUCCESS;
|
||||
}
|
||||
|
||||
@ -566,8 +557,8 @@ for the JavaScript code in this tag.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgfbe4bec" class="outline-3">
|
||||
<h3 id="orgfbe4bec"><span class="section-number-3">1.5</span> Template for HDF5 has/read/write a dataset of numerical data</h3>
|
||||
<div id="outline-container-orga702a5a" class="outline-3">
|
||||
<h3 id="orga702a5a"><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="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -696,8 +687,8 @@ for the JavaScript code in this tag.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org4197b20" class="outline-3">
|
||||
<h3 id="org4197b20"><span class="section-number-3">1.6</span> Template for HDF5 has/read/write a dataset of strings</h3>
|
||||
<div id="outline-container-org45c67c1" class="outline-3">
|
||||
<h3 id="org45c67c1"><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="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -901,8 +892,8 @@ for the JavaScript code in this tag.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org2d1e0a9" class="outline-3">
|
||||
<h3 id="org2d1e0a9"><span class="section-number-3">1.7</span> Template for HDF5 has/read/write a single string attribute</h3>
|
||||
<div id="outline-container-orgd1d2c79" class="outline-3">
|
||||
<h3 id="orgd1d2c79"><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="org-src-container">
|
||||
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
|
||||
@ -1029,7 +1020,7 @@ for the JavaScript code in this tag.
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2021-06-22 Tue 10:22</p>
|
||||
<p class="date">Created: 2021-06-22 Tue 20:32</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
@ -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>
|
||||
<!-- 2021-06-22 Tue 10:22 -->
|
||||
<!-- 2021-06-22 Tue 20:32 -->
|
||||
<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="#org6980a1d">1. TEXT back end</a>
|
||||
<li><a href="#org67d8a15">1. TEXT back end</a>
|
||||
<ul>
|
||||
<li><a href="#org4a956e8">1.1. Template for group-related structures 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="#org94ad673">1.3. Initialize function (constant part)</a></li>
|
||||
<li><a href="#orgf20c903">1.4. Deinitialize function (templated part)</a></li>
|
||||
<li><a href="#org948bec8">1.5. Template for text read struct</a></li>
|
||||
<li><a href="#orgfe865f3">1.6. Template for text flush struct</a></li>
|
||||
<li><a href="#org0485fc6">1.7. Template for text free memory</a></li>
|
||||
<li><a href="#org471f17d">1.8. Template for has/read/write the num attribute</a></li>
|
||||
<li><a href="#orgd83b77c">1.9. Template for has/read/write the dataset of numerical data</a></li>
|
||||
<li><a href="#orgbc536fa">1.10. Template for has/read/write the dataset of strings</a></li>
|
||||
<li><a href="#orga7e1cd1">1.11. Template for has/read/write the string attribute</a></li>
|
||||
<li><a href="#orgbe0f5b4">1.12. RDM struct (hard-coded)</a>
|
||||
<li><a href="#orgc4e0e70">1.1. Template for group-related structures in text back end</a></li>
|
||||
<li><a href="#orgc4ca588">1.2. Template for general structure in text back end</a></li>
|
||||
<li><a href="#org04d06cb">1.3. Initialize function (constant part)</a></li>
|
||||
<li><a href="#org26d0e21">1.4. Deinitialize function (templated part)</a></li>
|
||||
<li><a href="#orge9141ef">1.5. Template for text read struct</a></li>
|
||||
<li><a href="#orga04f98c">1.6. Template for text flush struct</a></li>
|
||||
<li><a href="#org4b0a49c">1.7. Template for text free memory</a></li>
|
||||
<li><a href="#orga9f8b7e">1.8. Template for has/read/write the num attribute</a></li>
|
||||
<li><a href="#org42adf76">1.9. Template for has/read/write the dataset of numerical data</a></li>
|
||||
<li><a href="#org210c59d">1.10. Template for has/read/write the dataset of strings</a></li>
|
||||
<li><a href="#org7933579">1.11. Template for has/read/write the string attribute</a></li>
|
||||
<li><a href="#org85cb9f0">1.12. RDM struct (hard-coded)</a>
|
||||
<ul>
|
||||
<li><a href="#org9ffc8b3">1.12.1. Read the complete struct</a></li>
|
||||
<li><a href="#org0173c0a">1.12.2. Flush the complete struct</a></li>
|
||||
<li><a href="#org3e69bab">1.12.3. Free memory</a></li>
|
||||
<li><a href="#org3e05553">1.12.4. Read/Write the one<sub>e</sub> attribute</a></li>
|
||||
<li><a href="#orgd901aa8">1.12.5. Read/Write the two<sub>e</sub> attribute</a></li>
|
||||
<li><a href="#orgcc5ce1b">1.12.1. Read the complete struct</a></li>
|
||||
<li><a href="#org5a08975">1.12.2. Flush the complete struct</a></li>
|
||||
<li><a href="#org8fa2a37">1.12.3. Free memory</a></li>
|
||||
<li><a href="#orgde85e26">1.12.4. Read/Write the one<sub>e</sub> attribute</a></li>
|
||||
<li><a href="#orge642eda">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-org6980a1d" class="outline-2">
|
||||
<h2 id="org6980a1d"><span class="section-number-2">1</span> TEXT back end</h2>
|
||||
<div id="outline-container-org67d8a15" class="outline-2">
|
||||
<h2 id="org67d8a15"><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-org4a956e8" class="outline-3">
|
||||
<h3 id="org4a956e8"><span class="section-number-3">1.1</span> Template for group-related structures in text back end</h3>
|
||||
<div id="outline-container-orgc4e0e70" class="outline-3">
|
||||
<h3 id="orgc4e0e70"><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 {
|
||||
@ -380,8 +380,8 @@ The file is written when closed, or when the flush function is called.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org1986736" class="outline-3">
|
||||
<h3 id="org1986736"><span class="section-number-3">1.2</span> Template for general structure in text back end</h3>
|
||||
<div id="outline-container-orgc4ca588" class="outline-3">
|
||||
<h3 id="orgc4ca588"><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> {
|
||||
@ -407,8 +407,8 @@ The file is written when closed, or when the flush function is called.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org94ad673" class="outline-3">
|
||||
<h3 id="org94ad673"><span class="section-number-3">1.3</span> Initialize function (constant part)</h3>
|
||||
<div id="outline-container-org04d06cb" class="outline-3">
|
||||
<h3 id="org04d06cb"><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>
|
||||
@ -509,8 +509,8 @@ The file is written when closed, or when the flush function is called.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgf20c903" class="outline-3">
|
||||
<h3 id="orgf20c903"><span class="section-number-3">1.4</span> Deinitialize function (templated part)</h3>
|
||||
<div id="outline-container-org26d0e21" class="outline-3">
|
||||
<h3 id="org26d0e21"><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>
|
||||
@ -535,8 +535,8 @@ The file is written when closed, or when the flush function is called.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org948bec8" class="outline-3">
|
||||
<h3 id="org948bec8"><span class="section-number-3">1.5</span> Template for text read struct</h3>
|
||||
<div id="outline-container-orge9141ef" class="outline-3">
|
||||
<h3 id="orge9141ef"><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*
|
||||
@ -807,8 +807,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgfe865f3" class="outline-3">
|
||||
<h3 id="orgfe865f3"><span class="section-number-3">1.6</span> Template for text flush struct</h3>
|
||||
<div id="outline-container-orga04f98c" class="outline-3">
|
||||
<h3 id="orga04f98c"><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>
|
||||
@ -872,8 +872,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org0485fc6" class="outline-3">
|
||||
<h3 id="org0485fc6"><span class="section-number-3">1.7</span> Template for text free memory</h3>
|
||||
<div id="outline-container-org4b0a49c" class="outline-3">
|
||||
<h3 id="org4b0a49c"><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.
|
||||
@ -918,8 +918,8 @@ Memory is allocated when reading. The following function frees memory.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org471f17d" class="outline-3">
|
||||
<h3 id="org471f17d"><span class="section-number-3">1.8</span> Template for has/read/write the num attribute</h3>
|
||||
<div id="outline-container-orga9f8b7e" class="outline-3">
|
||||
<h3 id="orga9f8b7e"><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="org-src-container">
|
||||
<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 id="outline-container-orgd83b77c" class="outline-3">
|
||||
<h3 id="orgd83b77c"><span class="section-number-3">1.9</span> Template for has/read/write the dataset of numerical data</h3>
|
||||
<div id="outline-container-org42adf76" class="outline-3">
|
||||
<h3 id="org42adf76"><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.
|
||||
@ -1078,8 +1078,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-orgbc536fa" class="outline-3">
|
||||
<h3 id="orgbc536fa"><span class="section-number-3">1.10</span> Template for has/read/write the dataset of strings</h3>
|
||||
<div id="outline-container-org210c59d" class="outline-3">
|
||||
<h3 id="org210c59d"><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.
|
||||
@ -1181,8 +1181,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-orga7e1cd1" class="outline-3">
|
||||
<h3 id="orga7e1cd1"><span class="section-number-3">1.11</span> Template for has/read/write the string attribute</h3>
|
||||
<div id="outline-container-org7933579" class="outline-3">
|
||||
<h3 id="org7933579"><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>
|
||||
@ -1256,12 +1256,12 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
</div>
|
||||
<div id="outline-container-orgbe0f5b4" class="outline-3">
|
||||
<h3 id="orgbe0f5b4"><span class="section-number-3">1.12</span> RDM struct (hard-coded)</h3>
|
||||
<div id="outline-container-org85cb9f0" class="outline-3">
|
||||
<h3 id="org85cb9f0"><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-org9ffc8b3" class="outline-4">
|
||||
<h4 id="org9ffc8b3"><span class="section-number-4">1.12.1</span> Read the complete struct</h4>
|
||||
<div id="outline-container-orgcc5ce1b" class="outline-4">
|
||||
<h4 id="orgcc5ce1b"><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>);
|
||||
@ -1356,8 +1356,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org0173c0a" class="outline-4">
|
||||
<h4 id="org0173c0a"><span class="section-number-4">1.12.2</span> Flush the complete struct</h4>
|
||||
<div id="outline-container-org5a08975" class="outline-4">
|
||||
<h4 id="org5a08975"><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>);
|
||||
@ -1399,8 +1399,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org3e69bab" class="outline-4">
|
||||
<h4 id="org3e69bab"><span class="section-number-4">1.12.3</span> Free memory</h4>
|
||||
<div id="outline-container-org8fa2a37" class="outline-4">
|
||||
<h4 id="org8fa2a37"><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.
|
||||
@ -1436,8 +1436,8 @@ Memory is allocated when reading. The followig function frees memory.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org3e05553" class="outline-4">
|
||||
<h4 id="org3e05553"><span class="section-number-4">1.12.4</span> Read/Write the one<sub>e</sub> attribute</h4>
|
||||
<div id="outline-container-orgde85e26" class="outline-4">
|
||||
<h4 id="orgde85e26"><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.
|
||||
@ -1503,8 +1503,8 @@ The <code>one_e</code> array is assumed allocated with the appropriate size.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgd901aa8" class="outline-4">
|
||||
<h4 id="orgd901aa8"><span class="section-number-4">1.12.5</span> Read/Write the two<sub>e</sub> attribute</h4>
|
||||
<div id="outline-container-orge642eda" class="outline-4">
|
||||
<h4 id="orge642eda"><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
|
||||
@ -1612,7 +1612,7 @@ file for each sparse float structure.
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2021-06-22 Tue 10:22</p>
|
||||
<p class="date">Created: 2021-06-22 Tue 20:32</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
118
trex.html
118
trex.html
@ -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>
|
||||
<!-- 2021-06-22 Tue 10:22 -->
|
||||
<!-- 2021-06-22 Tue 20:32 -->
|
||||
<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>
|
||||
@ -333,28 +333,28 @@ for the JavaScript code in this tag.
|
||||
<h2>Table of Contents</h2>
|
||||
<div id="text-table-of-contents">
|
||||
<ul>
|
||||
<li><a href="#org5279cdc">1. Metadata</a></li>
|
||||
<li><a href="#org0982faa">2. Electron</a></li>
|
||||
<li><a href="#org06148c9">3. Nucleus</a></li>
|
||||
<li><a href="#org1091334">4. <span class="todo TODO">TODO</span> Effective core potentials</a></li>
|
||||
<li><a href="#orgd468ddf">5. Basis set</a></li>
|
||||
<li><a href="#orgbd99e35">6. Atomic orbitals</a>
|
||||
<li><a href="#orgc08a996">1. Metadata</a></li>
|
||||
<li><a href="#orgfc6802e">2. Electron</a></li>
|
||||
<li><a href="#org89ad5cd">3. Nucleus</a></li>
|
||||
<li><a href="#orgb4ac0b7">4. <span class="todo TODO">TODO</span> Effective core potentials</a></li>
|
||||
<li><a href="#org86016e6">5. Basis set</a></li>
|
||||
<li><a href="#org96b16b7">6. Atomic orbitals</a>
|
||||
<ul>
|
||||
<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>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org80705e6">7. Molecular orbitals</a>
|
||||
<li><a href="#org2f3ed38">7. Molecular orbitals</a>
|
||||
<ul>
|
||||
<li><a href="#org887cd83">7.1. One-electron integrals</a></li>
|
||||
<li><a href="#orgf9a83b3">7.2. Two-electron integrals</a></li>
|
||||
<li><a href="#org72bc6af">7.1. One-electron integrals</a></li>
|
||||
<li><a href="#orgd1fde5a">7.2. Two-electron integrals</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
<li><a href="#org7ec2323">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
|
||||
<li><a href="#org067a381">9. <span class="todo TODO">TODO</span> Reduced density matrices</a></li>
|
||||
<li><a href="#orgba9a827">10. Appendix</a>
|
||||
<li><a href="#org22ac68f">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
|
||||
<li><a href="#org177ee41">9. <span class="todo TODO">TODO</span> Reduced density matrices</a></li>
|
||||
<li><a href="#orgbbdb680">10. Appendix</a>
|
||||
<ul>
|
||||
<li><a href="#org7facd3c">10.1. Python script from table to json</a></li>
|
||||
<li><a href="#orgca98b95">10.1. Python script from table to json</a></li>
|
||||
</ul>
|
||||
</li>
|
||||
</ul>
|
||||
@ -379,8 +379,8 @@ arrays are 0-base. Hence, we introduce the <code>index</code> type which is an
|
||||
</pre>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org5279cdc" class="outline-2">
|
||||
<h2 id="org5279cdc"><span class="section-number-2">1</span> Metadata</h2>
|
||||
<div id="outline-container-orgc08a996" class="outline-2">
|
||||
<h2 id="orgc08a996"><span class="section-number-2">1</span> Metadata</h2>
|
||||
<div class="outline-text-2" id="text-1">
|
||||
<p>
|
||||
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.
|
||||
</p>
|
||||
|
||||
<table id="orgdd683e1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgee436b4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -442,15 +442,15 @@ authors of the file, and a textual description.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org0982faa" class="outline-2">
|
||||
<h2 id="org0982faa"><span class="section-number-2">2</span> Electron</h2>
|
||||
<div id="outline-container-orgfc6802e" class="outline-2">
|
||||
<h2 id="orgfc6802e"><span class="section-number-2">2</span> Electron</h2>
|
||||
<div class="outline-text-2" id="text-2">
|
||||
<p>
|
||||
We consider wave functions expressed in the spin-free formalism, where
|
||||
the number of ↑ and ↓ electrons is fixed.
|
||||
</p>
|
||||
|
||||
<table id="org55d80d1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgee69920" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -481,15 +481,15 @@ the number of ↑ and ↓ electrons is fixed.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org06148c9" class="outline-2">
|
||||
<h2 id="org06148c9"><span class="section-number-2">3</span> Nucleus</h2>
|
||||
<div id="outline-container-org89ad5cd" class="outline-2">
|
||||
<h2 id="org89ad5cd"><span class="section-number-2">3</span> Nucleus</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="org88f35a6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org9732f69" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -541,8 +541,8 @@ given in Cartesian \((x,y,z)\) format.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org1091334" class="outline-2">
|
||||
<h2 id="org1091334"><span class="section-number-2">4</span> <span class="todo TODO">TODO</span> Effective core potentials</h2>
|
||||
<div id="outline-container-orgb4ac0b7" class="outline-2">
|
||||
<h2 id="orgb4ac0b7"><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">
|
||||
<p>
|
||||
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>
|
||||
</ul>
|
||||
|
||||
<table id="org2b19107" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org0701dfb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -688,8 +688,8 @@ letters are parameters.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgd468ddf" class="outline-2">
|
||||
<h2 id="orgd468ddf"><span class="section-number-2">5</span> Basis set</h2>
|
||||
<div id="outline-container-org86016e6" class="outline-2">
|
||||
<h2 id="org86016e6"><span class="section-number-2">5</span> Basis set</h2>
|
||||
<div class="outline-text-2" id="text-5">
|
||||
<p>
|
||||
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:
|
||||
</p>
|
||||
|
||||
<table id="orge01baf1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org5968aad" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -903,8 +903,8 @@ prim_factor =
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgbd99e35" class="outline-2">
|
||||
<h2 id="orgbd99e35"><span class="section-number-2">6</span> Atomic orbitals</h2>
|
||||
<div id="outline-container-org96b16b7" class="outline-2">
|
||||
<h2 id="org96b16b7"><span class="section-number-2">6</span> Atomic orbitals</h2>
|
||||
<div class="outline-text-2" id="text-6">
|
||||
<p>
|
||||
Going from the atomic basis set to AOs implies a systematic
|
||||
@ -952,13 +952,13 @@ shell, as in the GAMESS convention where
|
||||
|
||||
<p>
|
||||
In such a case, one should set the normalization of the shell (in
|
||||
the <a href="#orgd468ddf">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
|
||||
the <a href="#org86016e6">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="org339cf8f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgba83541" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1002,8 +1002,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgee50798" class="outline-3">
|
||||
<h3 id="ao_one_e"><a id="orgee50798"></a><span class="section-number-3">6.1</span> One-electron integrals</h3>
|
||||
<div id="outline-container-orge8be744" class="outline-3">
|
||||
<h3 id="ao_one_e"><a id="orge8be744"></a><span class="section-number-3">6.1</span> One-electron integrals</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}}
|
||||
@ -1021,7 +1021,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
|
||||
over atomic orbitals.
|
||||
</p>
|
||||
|
||||
<table id="orgdfd2e58" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org8a5916c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1080,8 +1080,8 @@ over atomic orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgf29d729" class="outline-3">
|
||||
<h3 id="ao_two_e"><a id="orgf29d729"></a><span class="section-number-3">6.2</span> Two-electron integrals</h3>
|
||||
<div id="outline-container-org1337252" class="outline-3">
|
||||
<h3 id="ao_two_e"><a id="org1337252"></a><span class="section-number-3">6.2</span> Two-electron integrals</h3>
|
||||
<div class="outline-text-3" id="text-ao_two_e">
|
||||
<p>
|
||||
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>
|
||||
</ul>
|
||||
|
||||
<table id="org0b07b1e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org9db7635" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1134,10 +1134,10 @@ notation.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org80705e6" class="outline-2">
|
||||
<h2 id="org80705e6"><span class="section-number-2">7</span> Molecular orbitals</h2>
|
||||
<div id="outline-container-org2f3ed38" class="outline-2">
|
||||
<h2 id="org2f3ed38"><span class="section-number-2">7</span> Molecular orbitals</h2>
|
||||
<div class="outline-text-2" id="text-7">
|
||||
<table id="org0334a09" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org2e94a16" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1195,8 +1195,8 @@ notation.
|
||||
</table>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org887cd83" class="outline-3">
|
||||
<h3 id="org887cd83"><span class="section-number-3">7.1</span> One-electron integrals</h3>
|
||||
<div id="outline-container-org72bc6af" class="outline-3">
|
||||
<h3 id="org72bc6af"><span class="section-number-3">7.1</span> One-electron integrals</h3>
|
||||
<div class="outline-text-3" id="text-7-1">
|
||||
<p>
|
||||
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.
|
||||
</p>
|
||||
|
||||
<table id="org5a122f1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org7bc73bb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1263,8 +1263,8 @@ the basis of molecular orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgf9a83b3" class="outline-3">
|
||||
<h3 id="orgf9a83b3"><span class="section-number-3">7.2</span> Two-electron integrals</h3>
|
||||
<div id="outline-container-orgd1fde5a" class="outline-3">
|
||||
<h3 id="orgd1fde5a"><span class="section-number-3">7.2</span> Two-electron integrals</h3>
|
||||
<div class="outline-text-3" id="text-7-2">
|
||||
<p>
|
||||
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.
|
||||
</p>
|
||||
|
||||
<table id="org6886615" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="org35a9ecf" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1304,13 +1304,13 @@ the basis of molecular orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-org7ec2323" class="outline-2">
|
||||
<h2 id="org7ec2323"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
|
||||
<div id="outline-container-org22ac68f" class="outline-2">
|
||||
<h2 id="org22ac68f"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
|
||||
</div>
|
||||
<div id="outline-container-org067a381" class="outline-2">
|
||||
<h2 id="org067a381"><span class="section-number-2">9</span> <span class="todo TODO">TODO</span> Reduced density matrices</h2>
|
||||
<div id="outline-container-org177ee41" class="outline-2">
|
||||
<h2 id="org177ee41"><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">
|
||||
<table id="org8158e45" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
<table id="orgdbd98ae" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
|
||||
|
||||
|
||||
<colgroup>
|
||||
@ -1349,15 +1349,15 @@ the basis of molecular orbitals.
|
||||
</div>
|
||||
</div>
|
||||
|
||||
<div id="outline-container-orgba9a827" class="outline-2">
|
||||
<h2 id="orgba9a827"><span class="section-number-2">10</span> Appendix</h2>
|
||||
<div id="outline-container-orgbbdb680" class="outline-2">
|
||||
<h2 id="orgbbdb680"><span class="section-number-2">10</span> Appendix</h2>
|
||||
<div class="outline-text-2" id="text-10">
|
||||
</div>
|
||||
<div id="outline-container-org7facd3c" class="outline-3">
|
||||
<h3 id="org7facd3c"><span class="section-number-3">10.1</span> Python script from table to json</h3>
|
||||
<div id="outline-container-orgca98b95" class="outline-3">
|
||||
<h3 id="orgca98b95"><span class="section-number-3">10.1</span> Python script from table to json</h3>
|
||||
<div class="outline-text-3" id="text-10-1">
|
||||
<div class="org-src-container">
|
||||
<pre class="src src-python" id="orgd0f52f2"><span style="color: #a020f0;">print</span>(<span style="color: #8b2252;">"""#+begin_src python :tangle trex.json"""</span>)
|
||||
<pre class="src src-python" id="org059451c"><span style="color: #a020f0;">print</span>(<span style="color: #8b2252;">"""#+begin_src python :tangle trex.json"""</span>)
|
||||
<span style="color: #a020f0;">print</span>(<span style="color: #8b2252;">""" "%s": {"""</span>%(title))
|
||||
<span style="color: #a0522d;">indent</span> = <span style="color: #8b2252;">" "</span>
|
||||
<span style="color: #a0522d;">f1</span> = 0 ; <span style="color: #a0522d;">f2</span> = 0 ; <span style="color: #a0522d;">f3</span> = 0
|
||||
@ -1416,7 +1416,7 @@ the basis of molecular orbitals.
|
||||
</div>
|
||||
<div id="postamble" class="status">
|
||||
<p class="author">Author: TREX-CoE</p>
|
||||
<p class="date">Created: 2021-06-22 Tue 10:22</p>
|
||||
<p class="date">Created: 2021-06-22 Tue 20:32</p>
|
||||
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
|
||||
</div>
|
||||
</body>
|
||||
|
||||
Loading…
Reference in New Issue
Block a user