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README.html
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<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>
@ -347,7 +347,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-01-13 Thu 12:27</p>
<p class="date">Created: 2022-01-17 Mon 18:16</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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<head>
<!-- 2022-01-13 Thu 12:27 -->
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Examples</title>
@ -333,24 +333,24 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgebcab34">1. Accessing sparse quantities</a>
<li><a href="#org67c71c7">1. Accessing sparse quantities</a>
<ul>
<li><a href="#org9322f63">1.1. Fortran</a>
<li><a href="#orgc08e4a1">1.1. Fortran</a>
<ul>
<li><a href="#org142cbe9">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org07cd7b9">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org8953486">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org1161056">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org1a23fb1">1.1.5. Allocate memory</a></li>
<li><a href="#org8e11593">1.1.6. Read one-electron quantities</a></li>
<li><a href="#org7abd4ea">1.1.7. Read two-electron quantities</a>
<li><a href="#org1f2dbb8">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org3d8c1f3">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org6924260">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orgd18e4be">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org7de3074">1.1.5. Allocate memory</a></li>
<li><a href="#org38d877c">1.1.6. Read one-electron quantities</a></li>
<li><a href="#orge2d8e2c">1.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#orgdc912ca">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#orgbf671ca">1.1.7.2. Reduced density matrix</a></li>
<li><a href="#org77b645d">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org8e79657">1.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org4f1143d">1.1.8. Compute the energy</a></li>
<li><a href="#orgf32e031">1.1.9. Terminate</a></li>
<li><a href="#org1839a31">1.1.8. Compute the energy</a></li>
<li><a href="#orge6f7009">1.1.9. Terminate</a></li>
</ul>
</li>
</ul>
@ -360,12 +360,12 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-orgebcab34" class="outline-2">
<h2 id="orgebcab34"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
<div id="outline-container-org67c71c7" class="outline-2">
<h2 id="org67c71c7"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-org9322f63" class="outline-3">
<h3 id="org9322f63"><span class="section-number-3">1.1</span> Fortran</h3>
<div id="outline-container-orgc08e4a1" class="outline-3">
<h3 id="orgc08e4a1"><span class="section-number-3">1.1</span> Fortran</h3>
<div class="outline-text-3" id="text-1-1">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">print_energy</span>
@ -411,8 +411,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org142cbe9" class="outline-4">
<h4 id="org142cbe9"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org1f2dbb8" class="outline-4">
<h4 id="org1f2dbb8"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div class="outline-text-4" id="text-1-1-1">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #228b22;">integer</span> ::<span style="color: #a0522d;"> i, j, k, l, m</span>
@ -427,8 +427,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org07cd7b9" class="outline-4">
<h4 id="org07cd7b9"><span class="section-number-4">1.1.2</span> Obtain the name of the TREXIO file from the command line, and open it for reading</h4>
<div id="outline-container-org3d8c1f3" class="outline-4">
<h4 id="org3d8c1f3"><span class="section-number-4">1.1.2</span> Obtain the name of the TREXIO file from the command line, and open it for reading</h4>
<div class="outline-text-4" id="text-1-1-2">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">call</span> <span style="color: #0000ff;">getarg</span>(1, filename)
@ -444,8 +444,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-org8953486" class="outline-4">
<h4 id="org8953486"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org6924260" class="outline-4">
<h4 id="org6924260"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div class="outline-text-4" id="text-1-1-3">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_read_nucleus_repulsion(f, E_nn)
@ -459,8 +459,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-org1161056" class="outline-4">
<h4 id="org1161056"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-orgd18e4be" class="outline-4">
<h4 id="orgd18e4be"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div class="outline-text-4" id="text-1-1-4">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_read_mo_num(f, n)
@ -474,8 +474,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-org1a23fb1" class="outline-4">
<h4 id="org1a23fb1"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div id="outline-container-org7de3074" class="outline-4">
<h4 id="org7de3074"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div class="outline-text-4" id="text-1-1-5">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">allocate</span>( D(n,n), h0(n,n) )
@ -487,8 +487,8 @@ W(:,:,:,:) = 0.d0
</div>
</div>
<div id="outline-container-org8e11593" class="outline-4">
<h4 id="org8e11593"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org38d877c" class="outline-4">
<h4 id="org38d877c"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div class="outline-text-4" id="text-1-1-6">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_has_mo_1e_int_core_hamiltonian(f)
@ -520,8 +520,8 @@ rc = trexio_read_rdm_1e(f, D)
</div>
</div>
<div id="outline-container-org7abd4ea" class="outline-4">
<h4 id="org7abd4ea"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-orge2d8e2c" class="outline-4">
<h4 id="orge2d8e2c"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div class="outline-text-4" id="text-1-1-7">
<p>
Reading is done with OpenMP. Each thread reads its own buffer, and
@ -537,8 +537,8 @@ to be protected in the critical section when modified.
</p>
</div>
<div id="outline-container-orgdc912ca" class="outline-5">
<h5 id="orgdc912ca"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org77b645d" class="outline-5">
<h5 id="org77b645d"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div class="outline-text-5" id="text-1-1-7-1">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_has_mo_2e_int_eri(f)
@ -587,8 +587,8 @@ icount = BUFSIZE
</div>
</div>
<div id="outline-container-orgbf671ca" class="outline-5">
<h5 id="orgbf671ca"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org8e79657" class="outline-5">
<h5 id="org8e79657"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div class="outline-text-5" id="text-1-1-7-2">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_has_rdm_2e(f)
@ -632,8 +632,8 @@ icount = bufsize
</div>
</div>
<div id="outline-container-org4f1143d" class="outline-4">
<h4 id="org4f1143d"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div id="outline-container-org1839a31" class="outline-4">
<h4 id="org1839a31"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div class="outline-text-4" id="text-1-1-8">
<p>
When the orbitals are real, we can use
@ -679,8 +679,8 @@ E = E + E_nn
</div>
</div>
<div id="outline-container-orgf32e031" class="outline-4">
<h4 id="orgf32e031"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div id="outline-container-orge6f7009" class="outline-4">
<h4 id="orge6f7009"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div class="outline-text-4" id="text-1-1-9">
<div class="org-src-container">
<pre class="src src-f90"> <span style="color: #a020f0;">deallocate</span>( D, h0, G, W )
@ -695,7 +695,7 @@ E = E + E_nn
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-01-13 Thu 12:27</p>
<p class="date">Created: 2022-01-17 Mon 18:16</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>
<!-- 2022-01-13 Thu 12:27 -->
<!-- 2022-01-17 Mon 18:16 -->
<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>
@ -347,7 +347,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-01-13 Thu 12:27</p>
<p class="date">Created: 2022-01-17 Mon 18:16</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-01-13 Thu 12:27 -->
<!-- 2022-01-17 Mon 18:15 -->
<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>
@ -333,131 +333,131 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgc24b545">1. Coding conventions</a>
<li><a href="#org4d414df">1. Coding conventions</a>
<ul>
<li><a href="#org9970742">1.1. Memory allocation</a></li>
<li><a href="#orge9fa27c">1.1. Memory allocation</a></li>
</ul>
</li>
<li><a href="#org2d8a210">2. Front end</a>
<li><a href="#org8f4f17a">2. Front end</a>
<ul>
<li><a href="#org6d6b530">2.1. Error handling</a>
<li><a href="#org7113c56">2.1. Error handling</a>
<ul>
<li><a href="#org2b6d3bd">2.1.1. Decoding errors</a>
<li><a href="#org106e629">2.1.1. Decoding errors</a>
<ul>
<li><a href="#org819a54d">2.1.1.1. C source code</a></li>
<li><a href="#org6cd2679">2.1.1.2. Fortran interface</a></li>
<li><a href="#org6ce9baf">2.1.1.3. Python interface</a></li>
<li><a href="#org6144a9c">2.1.1.1. C source code</a></li>
<li><a href="#orgc74e3d6">2.1.1.2. Fortran interface</a></li>
<li><a href="#orga4a3bea">2.1.1.3. Python interface</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org634fb72">2.2. Back ends</a>
<li><a href="#org393faf8">2.2. Back ends</a>
<ul>
<li><a href="#org7f9d922">2.2.1. C</a></li>
<li><a href="#org528a791">2.2.2. Fortran</a></li>
<li><a href="#orge41ae4c">2.2.3. Python</a></li>
<li><a href="#org569ad16">2.2.1. C</a></li>
<li><a href="#org04e3e0d">2.2.2. Fortran</a></li>
<li><a href="#org87e3ce9">2.2.3. Python</a></li>
</ul>
</li>
<li><a href="#orgc3e43ea">2.3. Read/write behavior</a></li>
<li><a href="#org5a13e96">2.4. TREXIO file type</a>
<li><a href="#org471d9da">2.3. Read/write behavior</a></li>
<li><a href="#orgd642525">2.4. TREXIO file type</a>
<ul>
<li><a href="#org0559be2">2.4.1. TREXIO<sub>File</sub> Python class</a></li>
<li><a href="#orgaf2763e">2.4.1. TREXIO<sub>File</sub> Python class</a></li>
</ul>
</li>
<li><a href="#org946533f">2.5. Polymorphism of the file handle</a></li>
<li><a href="#org0e24bcb">2.6. File opening</a>
<li><a href="#org3815905">2.5. Polymorphism of the file handle</a></li>
<li><a href="#org863bdee">2.6. File opening</a>
<ul>
<li><a href="#orgd759c12">2.6.1. C</a></li>
<li><a href="#org9201fc7">2.6.2. Fortran</a></li>
<li><a href="#org293a3d2">2.6.3. Python</a></li>
<li><a href="#orgfb08a3c">2.6.4. Zero-based versus one-based arrays of indices</a></li>
<li><a href="#org5a496d2">2.6.1. C</a></li>
<li><a href="#orgcbb9c8b">2.6.2. Fortran</a></li>
<li><a href="#org696d280">2.6.3. Python</a></li>
<li><a href="#org81ac416">2.6.4. Zero-based versus one-based arrays of indices</a></li>
</ul>
</li>
<li><a href="#org29e3144">2.7. File closing</a>
<li><a href="#org49d42d7">2.7. File closing</a>
<ul>
<li><a href="#org5c50bd4">2.7.1. C</a></li>
<li><a href="#org275a2fd">2.7.2. Fortran</a></li>
<li><a href="#org0692d41">2.7.3. Python</a></li>
<li><a href="#org90ea770">2.7.1. C</a></li>
<li><a href="#orgf8cbf5d">2.7.2. Fortran</a></li>
<li><a href="#orge6e19fc">2.7.3. Python</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org26770b1">3. Templates for front end</a>
<li><a href="#orga92b9a9">3. Templates for front end</a>
<ul>
<li><a href="#org1e6a1c9">3.1. Description</a></li>
<li><a href="#org27ff88b">3.2. Templates for front end has/read/write a single numerical attribute</a>
<li><a href="#org5ad4e69">3.1. Description</a></li>
<li><a href="#org4de28d9">3.2. Templates for front end has/read/write a single numerical attribute</a>
<ul>
<li><a href="#orgd96a38c">3.2.1. Introduction</a></li>
<li><a href="#org1552750">3.2.2. C templates for front end</a>
<li><a href="#orgaeaaa9b">3.2.1. Introduction</a></li>
<li><a href="#org582ae09">3.2.2. C templates for front end</a>
<ul>
<li><a href="#org81df178">3.2.2.1. Function declarations</a></li>
<li><a href="#orgd63334b">3.2.2.2. Source code for double precision functions</a></li>
<li><a href="#org628d5c1">3.2.2.3. Source code for single precision functions</a></li>
<li><a href="#org7456afa">3.2.2.4. Source code for default functions</a></li>
<li><a href="#org8311cf0">3.2.2.1. Function declarations</a></li>
<li><a href="#orgb5464e5">3.2.2.2. Source code for double precision functions</a></li>
<li><a href="#org4794663">3.2.2.3. Source code for single precision functions</a></li>
<li><a href="#orgcdddccc">3.2.2.4. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#orgf699c0a">3.2.3. Fortran templates for front end</a></li>
<li><a href="#orgcb4daba">3.2.4. Python templates for front end</a></li>
<li><a href="#orgf559dad">3.2.3. Fortran templates for front end</a></li>
<li><a href="#orga8ee6da">3.2.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#orgcedf6cf">3.3. Templates for front end has/read/write a dataset of numerical data</a>
<li><a href="#org79a6099">3.3. Templates for front end has/read/write a dataset of numerical data</a>
<ul>
<li><a href="#org79613e2">3.3.1. Introduction</a></li>
<li><a href="#orgc6db6a8">3.3.2. C templates for front end</a>
<li><a href="#org7296ab4">3.3.1. Introduction</a></li>
<li><a href="#orgceee3cd">3.3.2. C templates for front end</a>
<ul>
<li><a href="#org7dc8e91">3.3.2.1. Function declarations</a></li>
<li><a href="#org28b3642">3.3.2.2. Source code for double precision functions</a></li>
<li><a href="#org4fb0ffc">3.3.2.3. Source code for single precision functions</a></li>
<li><a href="#orgd506abb">3.3.2.4. Source code for memory-safe functions</a></li>
<li><a href="#orgc72a89f">3.3.2.5. Source code for default functions</a></li>
<li><a href="#orgedf7b2b">3.3.2.1. Function declarations</a></li>
<li><a href="#org4686658">3.3.2.2. Source code for double precision functions</a></li>
<li><a href="#orged99113">3.3.2.3. Source code for single precision functions</a></li>
<li><a href="#orgecbbf28">3.3.2.4. Source code for memory-safe functions</a></li>
<li><a href="#orgc3f84cd">3.3.2.5. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#org637f67c">3.3.3. Fortran templates for front end</a></li>
<li><a href="#org71ac87c">3.3.4. Python templates for front end</a></li>
<li><a href="#orgfa99aae">3.3.3. Fortran templates for front end</a></li>
<li><a href="#org136cad8">3.3.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#orgc8cbdc2">3.4. Templates for front end has/read/write a dataset of sparse data</a>
<li><a href="#org6540cb5">3.4. Templates for front end has/read/write a dataset of sparse data</a>
<ul>
<li><a href="#org2dbd6d8">3.4.1. Introduction</a></li>
<li><a href="#org3bb54f2">3.4.2. C templates for front end</a>
<li><a href="#org2f58eed">3.4.1. Introduction</a></li>
<li><a href="#orgb32c4f0">3.4.2. C templates for front end</a>
<ul>
<li><a href="#org3852d3e">3.4.2.1. Function declarations</a></li>
<li><a href="#org78a9a48">3.4.2.2. Source code for default functions</a></li>
<li><a href="#orgec6d9b9">3.4.2.1. Function declarations</a></li>
<li><a href="#orga742e79">3.4.2.2. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#org8d4827e">3.4.3. Fortran templates for front end</a></li>
<li><a href="#org66e5208">3.4.4. Python templates for front end</a></li>
<li><a href="#org8590459">3.4.3. Fortran templates for front end</a></li>
<li><a href="#org4a68a2f">3.4.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#org5a110dd">3.5. Templates for front end has/read/write a dataset of strings</a>
<li><a href="#org88c4fb9">3.5. Templates for front end has/read/write a dataset of strings</a>
<ul>
<li><a href="#org707985c">3.5.1. Introduction</a></li>
<li><a href="#org0bf2bdd">3.5.2. C templates for front end</a>
<li><a href="#org12c9e0b">3.5.1. Introduction</a></li>
<li><a href="#orga05bc97">3.5.2. C templates for front end</a>
<ul>
<li><a href="#orgc2a964b">3.5.2.1. Function declarations</a></li>
<li><a href="#orgc8b7ab8">3.5.2.2. Source code for default functions</a></li>
<li><a href="#org95700d6">3.5.2.1. Function declarations</a></li>
<li><a href="#orgb137ac6">3.5.2.2. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#orga0d6452">3.5.3. Fortran templates for front end</a></li>
<li><a href="#orgf5bdd7b">3.5.4. Python templates for front end</a></li>
<li><a href="#orgfdbd72d">3.5.3. Fortran templates for front end</a></li>
<li><a href="#orgb4947fc">3.5.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#org7efbca8">3.6. Templates for front end has/read/write a single string attribute</a>
<li><a href="#orgbb467e6">3.6. Templates for front end has/read/write a single string attribute</a>
<ul>
<li><a href="#orgcc07c9c">3.6.1. Introduction</a></li>
<li><a href="#org84f0c73">3.6.2. C templates for front end</a>
<li><a href="#org5b1ba3b">3.6.1. Introduction</a></li>
<li><a href="#orgafa3aea">3.6.2. C templates for front end</a>
<ul>
<li><a href="#org62a6779">3.6.2.1. Function declarations</a></li>
<li><a href="#orgee74d21">3.6.2.2. Source code for default functions</a></li>
<li><a href="#org8611a9b">3.6.2.1. Function declarations</a></li>
<li><a href="#orgf159f96">3.6.2.2. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#org381b62d">3.6.3. Fortran templates for front end</a></li>
<li><a href="#org92b4376">3.6.4. Python templates for front end</a></li>
<li><a href="#orgc7a4f33">3.6.3. Fortran templates for front end</a></li>
<li><a href="#orga258076">3.6.4. Python templates for front end</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org37cddcc">4. Fortran helper/wrapper functions</a></li>
<li><a href="#orgfd9b6ad">4. Fortran helper/wrapper functions</a></li>
</ul>
</div>
</div>
@ -465,8 +465,8 @@ for the JavaScript code in this tag.
break;
</p>
<div id="outline-container-orgc24b545" class="outline-2">
<h2 id="orgc24b545"><span class="section-number-2">1</span> Coding conventions</h2>
<div id="outline-container-org4d414df" class="outline-2">
<h2 id="org4d414df"><span class="section-number-2">1</span> Coding conventions</h2>
<div class="outline-text-2" id="text-1">
<ul class="org-ul">
<li>integer types will be defined using types given in <code>stdint.h</code></li>
@ -481,8 +481,8 @@ break;
</ul>
</div>
<div id="outline-container-org9970742" class="outline-3">
<h3 id="org9970742"><span class="section-number-3">1.1</span> Memory allocation</h3>
<div id="outline-container-orge9fa27c" class="outline-3">
<h3 id="orge9fa27c"><span class="section-number-3">1.1</span> Memory allocation</h3>
<div class="outline-text-3" id="text-1-1">
<p>
Memory allocation of structures can be facilitated by using the
@ -517,8 +517,8 @@ The maximum string size for the filenames is 4096 characters.
</div>
</div>
<div id="outline-container-org2d8a210" class="outline-2">
<h2 id="org2d8a210"><span class="section-number-2">2</span> Front end</h2>
<div id="outline-container-org8f4f17a" class="outline-2">
<h2 id="org8f4f17a"><span class="section-number-2">2</span> Front end</h2>
<div class="outline-text-2" id="text-2">
<p>
All calls to TREXIO are thread-safe.
@ -526,10 +526,10 @@ TREXIO front end is modular, which simplifies implementation of new back ends.
</p>
</div>
<div id="outline-container-org6d6b530" class="outline-3">
<h3 id="org6d6b530"><span class="section-number-3">2.1</span> Error handling</h3>
<div id="outline-container-org7113c56" class="outline-3">
<h3 id="org7113c56"><span class="section-number-3">2.1</span> Error handling</h3>
<div class="outline-text-3" id="text-2-1">
<table id="org128f1ee" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgbb5567e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -770,8 +770,8 @@ and the corresponding message are not propagated to the source code.
</div>
</div>
<div id="outline-container-org2b6d3bd" class="outline-4">
<h4 id="org2b6d3bd"><span class="section-number-4">2.1.1</span> Decoding errors</h4>
<div id="outline-container-org106e629" class="outline-4">
<h4 id="org106e629"><span class="section-number-4">2.1.1</span> Decoding errors</h4>
<div class="outline-text-4" id="text-2-1-1">
<p>
The <code>trexio_string_of_error</code> converts an exit code into a string. The
@ -797,8 +797,8 @@ and the corresponding message are not propagated to the source code.
</p>
</div>
<div id="outline-container-org819a54d" class="outline-5">
<h5 id="org819a54d"><span class="section-number-5">2.1.1.1</span> C source code</h5>
<div id="outline-container-org6144a9c" class="outline-5">
<h5 id="org6144a9c"><span class="section-number-5">2.1.1.1</span> C source code</h5>
<div class="outline-text-5" id="text-2-1-1-1">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #a020f0;">const</span> <span style="color: #228b22;">char</span>*
@ -909,8 +909,8 @@ and the corresponding message are not propagated to the source code.
</div>
</div>
<div id="outline-container-org6cd2679" class="outline-5">
<h5 id="org6cd2679"><span class="section-number-5">2.1.1.2</span> Fortran interface</h5>
<div id="outline-container-orgc74e3d6" class="outline-5">
<h5 id="orgc74e3d6"><span class="section-number-5">2.1.1.2</span> Fortran interface</h5>
<div class="outline-text-5" id="text-2-1-1-2">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">interface</span>
@ -926,8 +926,8 @@ and the corresponding message are not propagated to the source code.
</div>
</div>
<div id="outline-container-org6ce9baf" class="outline-5">
<h5 id="org6ce9baf"><span class="section-number-5">2.1.1.3</span> Python interface</h5>
<div id="outline-container-orga4a3bea" class="outline-5">
<h5 id="orga4a3bea"><span class="section-number-5">2.1.1.3</span> Python interface</h5>
<div class="outline-text-5" id="text-2-1-1-3">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">class</span> <span style="color: #228b22;">Error</span>(<span style="color: #228b22;">Exception</span>):
@ -966,8 +966,8 @@ and the corresponding message are not propagated to the source code.
</div>
</div>
<div id="outline-container-org634fb72" class="outline-3">
<h3 id="org634fb72"><span class="section-number-3">2.2</span> Back ends</h3>
<div id="outline-container-org393faf8" class="outline-3">
<h3 id="org393faf8"><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:
@ -991,8 +991,8 @@ lines that correspond to the <code>TREXIO_JSON</code> back end (not implemented
</p>
</div>
<div id="outline-container-org7f9d922" class="outline-4">
<h4 id="org7f9d922"><span class="section-number-4">2.2.1</span> C</h4>
<div id="outline-container-org569ad16" class="outline-4">
<h4 id="org569ad16"><span class="section-number-4">2.2.1</span> C</h4>
<div class="outline-text-4" id="text-2-2-1">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #a020f0;">typedef</span> <span style="color: #228b22;">int32_t</span> <span style="color: #228b22;">back_end_t</span>;
@ -1035,8 +1035,8 @@ This is useful due to the fact that HDF5 back end can be disabled at configure s
</div>
</div>
<div id="outline-container-org528a791" class="outline-4">
<h4 id="org528a791"><span class="section-number-4">2.2.2</span> Fortran</h4>
<div id="outline-container-org04e3e0d" class="outline-4">
<h4 id="org04e3e0d"><span class="section-number-4">2.2.2</span> Fortran</h4>
<div class="outline-text-4" id="text-2-2-2">
<div class="org-src-container">
<pre class="src src-f90"> <span style="color: #228b22;">integer</span>(trexio_backend), <span style="color: #a020f0;">parameter</span> ::<span style="color: #a0522d;"> TREXIO_HDF5 = 0</span>
@ -1062,8 +1062,8 @@ The function below is a Fortran interface for the aforementioned C-compatible <c
</div>
</div>
<div id="outline-container-orge41ae4c" class="outline-4">
<h4 id="orge41ae4c"><span class="section-number-4">2.2.3</span> Python</h4>
<div id="outline-container-org87e3ce9" class="outline-4">
<h4 id="org87e3ce9"><span class="section-number-4">2.2.3</span> Python</h4>
<div class="outline-text-4" id="text-2-2-3">
<div class="org-src-container">
<pre class="src src-python"># <span style="color: #b22222;">define TREXIO back ends</span>
@ -1077,8 +1077,8 @@ The function below is a Fortran interface for the aforementioned C-compatible <c
</div>
</div>
<div id="outline-container-orgc3e43ea" class="outline-3">
<h3 id="orgc3e43ea"><span class="section-number-3">2.3</span> Read/write behavior</h3>
<div id="outline-container-org471d9da" class="outline-3">
<h3 id="org471d9da"><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
@ -1106,8 +1106,8 @@ concurrent programs, the behavior is not specified.
</p>
</div>
</div>
<div id="outline-container-org5a13e96" class="outline-3">
<h3 id="org5a13e96"><span class="section-number-3">2.4</span> TREXIO file type</h3>
<div id="outline-container-orgd642525" class="outline-3">
<h3 id="orgd642525"><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
@ -1141,8 +1141,8 @@ TREXIO files will have as a first argument the TREXIO file handle.
</div>
</div>
<div id="outline-container-org0559be2" class="outline-4">
<h4 id="org0559be2"><span class="section-number-4">2.4.1</span> TREXIO<sub>File</sub> Python class</h4>
<div id="outline-container-orgaf2763e" class="outline-4">
<h4 id="orgaf2763e"><span class="section-number-4">2.4.1</span> TREXIO<sub>File</sub> Python class</h4>
<div class="outline-text-4" id="text-2-4-1">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">class</span> <span style="color: #228b22;">File</span>:
@ -1215,8 +1215,8 @@ TREXIO files will have as a first argument the TREXIO file handle.
</div>
</div>
<div id="outline-container-org946533f" class="outline-3">
<h3 id="org946533f"><span class="section-number-3">2.5</span> Polymorphism of the file handle</h3>
<div id="outline-container-org3815905" class="outline-3">
<h3 id="org3815905"><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
@ -1235,8 +1235,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org0e24bcb" class="outline-3">
<h3 id="org0e24bcb"><span class="section-number-3">2.6</span> File opening</h3>
<div id="outline-container-org863bdee" class="outline-3">
<h3 id="org863bdee"><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.
@ -1275,8 +1275,8 @@ renaming the <code>.txt</code> data files.
</p>
</div>
<div id="outline-container-orgd759c12" class="outline-4">
<h4 id="orgd759c12"><span class="section-number-4">2.6.1</span> C</h4>
<div id="outline-container-org5a496d2" class="outline-4">
<h4 id="org5a496d2"><span class="section-number-4">2.6.1</span> C</h4>
<div class="outline-text-4" id="text-2-6-1">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_t</span>*
@ -1463,8 +1463,8 @@ renaming the <code>.txt</code> data files.
</div>
</div>
<div id="outline-container-org9201fc7" class="outline-4">
<h4 id="org9201fc7"><span class="section-number-4">2.6.2</span> Fortran</h4>
<div id="outline-container-orgcbb9c8b" class="outline-4">
<h4 id="orgcbb9c8b"><span class="section-number-4">2.6.2</span> Fortran</h4>
<div class="outline-text-4" id="text-2-6-2">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">interface</span>
@ -1482,8 +1482,8 @@ renaming the <code>.txt</code> data files.
</div>
</div>
<div id="outline-container-org293a3d2" class="outline-4">
<h4 id="org293a3d2"><span class="section-number-4">2.6.3</span> Python</h4>
<div id="outline-container-org696d280" class="outline-4">
<h4 id="org696d280"><span class="section-number-4">2.6.3</span> Python</h4>
<div class="outline-text-4" id="text-2-6-3">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">def</span> <span style="color: #0000ff;">open</span>(file_name: <span style="color: #483d8b;">str</span>, mode: <span style="color: #483d8b;">str</span>, back_end: <span style="color: #483d8b;">int</span>):
@ -1531,8 +1531,8 @@ renaming the <code>.txt</code> data files.
</div>
</div>
<div id="outline-container-orgfb08a3c" class="outline-4">
<h4 id="orgfb08a3c"><span class="section-number-4">2.6.4</span> Zero-based versus one-based arrays of indices</h4>
<div id="outline-container-org81ac416" class="outline-4">
<h4 id="org81ac416"><span class="section-number-4">2.6.4</span> Zero-based versus one-based arrays of indices</h4>
<div class="outline-text-4" id="text-2-6-4">
<p>
Because arrays are zero-based in Fortran, we need to set a flag to
@ -1565,8 +1565,8 @@ know if we need to shift by 1 arrays of indices.
</div>
</div>
<div id="outline-container-org29e3144" class="outline-3">
<h3 id="org29e3144"><span class="section-number-3">2.7</span> File closing</h3>
<div id="outline-container-org49d42d7" class="outline-3">
<h3 id="org49d42d7"><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.
@ -1583,8 +1583,8 @@ output:
</p>
</div>
<div id="outline-container-org5c50bd4" class="outline-4">
<h4 id="org5c50bd4"><span class="section-number-4">2.7.1</span> C</h4>
<div id="outline-container-org90ea770" class="outline-4">
<h4 id="org90ea770"><span class="section-number-4">2.7.1</span> C</h4>
<div class="outline-text-4" id="text-2-7-1">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1665,8 +1665,8 @@ output:
</div>
</div>
<div id="outline-container-org275a2fd" class="outline-4">
<h4 id="org275a2fd"><span class="section-number-4">2.7.2</span> Fortran</h4>
<div id="outline-container-orgf8cbf5d" class="outline-4">
<h4 id="orgf8cbf5d"><span class="section-number-4">2.7.2</span> Fortran</h4>
<div class="outline-text-4" id="text-2-7-2">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">interface</span>
@ -1680,8 +1680,8 @@ output:
</div>
</div>
<div id="outline-container-org0692d41" class="outline-4">
<h4 id="org0692d41"><span class="section-number-4">2.7.3</span> Python</h4>
<div id="outline-container-orge6e19fc" class="outline-4">
<h4 id="orge6e19fc"><span class="section-number-4">2.7.3</span> Python</h4>
<div class="outline-text-4" id="text-2-7-3">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">def</span> <span style="color: #0000ff;">close</span>(trexio_file):
@ -1703,12 +1703,12 @@ output:
</div>
</div>
<div id="outline-container-org26770b1" class="outline-2">
<h2 id="org26770b1"><span class="section-number-2">3</span> Templates for front end</h2>
<div id="outline-container-orga92b9a9" class="outline-2">
<h2 id="orga92b9a9"><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-org1e6a1c9" class="outline-3">
<h3 id="org1e6a1c9"><span class="section-number-3">3.1</span> Description</h3>
<div id="outline-container-org5ad4e69" class="outline-3">
<h3 id="org5ad4e69"><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>:
@ -1929,12 +1929,12 @@ value will result in <code>TREXIO_INVALID_ARG_2</code> exit code.
</div>
</div>
<div id="outline-container-org27ff88b" class="outline-3">
<h3 id="org27ff88b"><span class="section-number-3">3.2</span> Templates for front end has/read/write a single numerical attribute</h3>
<div id="outline-container-org4de28d9" class="outline-3">
<h3 id="org4de28d9"><span class="section-number-3">3.2</span> Templates for front end has/read/write a single numerical attribute</h3>
<div class="outline-text-3" id="text-3-2">
</div>
<div id="outline-container-orgd96a38c" class="outline-4">
<h4 id="orgd96a38c"><span class="section-number-4">3.2.1</span> Introduction</h4>
<div id="outline-container-orgaeaaa9b" class="outline-4">
<h4 id="orgaeaaa9b"><span class="section-number-4">3.2.1</span> Introduction</h4>
<div class="outline-text-4" id="text-3-2-1">
<p>
This section concerns API calls related to numerical attributes,
@ -2005,8 +2005,8 @@ namely single value of int/float types.
</div>
</div>
<div id="outline-container-org1552750" class="outline-4">
<h4 id="org1552750"><span class="section-number-4">3.2.2</span> C templates for front end</h4>
<div id="outline-container-org582ae09" class="outline-4">
<h4 id="org582ae09"><span class="section-number-4">3.2.2</span> C templates for front end</h4>
<div class="outline-text-4" id="text-3-2-2">
<p>
The <code>C</code> templates that correspond to each of the abovementioned
@ -2020,12 +2020,12 @@ precision (see Table above).
</p>
</div>
<div id="outline-container-org81df178" class="outline-5">
<h5 id="org81df178"><span class="section-number-5">3.2.2.1</span> Function declarations</h5>
<div id="outline-container-org8311cf0" class="outline-5">
<h5 id="org8311cf0"><span class="section-number-5">3.2.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-orgd63334b" class="outline-5">
<h5 id="orgd63334b"><span class="section-number-5">3.2.2.2</span> Source code for double precision functions</h5>
<div id="outline-container-orgb5464e5" class="outline-5">
<h5 id="orgb5464e5"><span class="section-number-5">3.2.2.2</span> Source code for double precision functions</h5>
<div class="outline-text-5" id="text-3-2-2-2">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -2088,8 +2088,8 @@ precision (see Table above).
</div>
</div>
<div id="outline-container-org628d5c1" class="outline-5">
<h5 id="org628d5c1"><span class="section-number-5">3.2.2.3</span> Source code for single precision functions</h5>
<div id="outline-container-org4794663" class="outline-5">
<h5 id="org4794663"><span class="section-number-5">3.2.2.3</span> Source code for single precision functions</h5>
<div class="outline-text-5" id="text-3-2-2-3">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -2164,8 +2164,8 @@ precision (see Table above).
</div>
</div>
<div id="outline-container-org7456afa" class="outline-5">
<h5 id="org7456afa"><span class="section-number-5">3.2.2.4</span> Source code for default functions</h5>
<div id="outline-container-orgcdddccc" class="outline-5">
<h5 id="orgcdddccc"><span class="section-number-5">3.2.2.4</span> Source code for default functions</h5>
<div class="outline-text-5" id="text-3-2-2-4">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -2220,8 +2220,8 @@ precision (see Table above).
</div>
</div>
<div id="outline-container-orgf699c0a" class="outline-4">
<h4 id="orgf699c0a"><span class="section-number-4">3.2.3</span> Fortran templates for front end</h4>
<div id="outline-container-orgf559dad" class="outline-4">
<h4 id="orgf559dad"><span class="section-number-4">3.2.3</span> Fortran templates for front end</h4>
<div class="outline-text-4" id="text-3-2-3">
<p>
The <code>Fortran</code> templates that provide an access to the <code>C</code> API calls from Fortran.
@ -2306,8 +2306,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-orgcb4daba" class="outline-4">
<h4 id="orgcb4daba"><span class="section-number-4">3.2.4</span> Python templates for front end</h4>
<div id="outline-container-orga8ee6da" class="outline-4">
<h4 id="orga8ee6da"><span class="section-number-4">3.2.4</span> Python templates for front end</h4>
<div class="outline-text-4" id="text-3-2-4">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">def</span> <span style="color: #0000ff;">write_</span>$group_num$(trexio_file, num_w: $group_num_py_dtype$) -&gt; <span style="color: #008b8b;">None</span>:
@ -2392,12 +2392,12 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-orgcedf6cf" class="outline-3">
<h3 id="orgcedf6cf"><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-org79a6099" class="outline-3">
<h3 id="org79a6099"><span class="section-number-3">3.3</span> Templates for front end has/read/write a dataset of numerical data</h3>
<div class="outline-text-3" id="text-3-3">
</div>
<div id="outline-container-org79613e2" class="outline-4">
<h4 id="org79613e2"><span class="section-number-4">3.3.1</span> Introduction</h4>
<div id="outline-container-org7296ab4" class="outline-4">
<h4 id="org7296ab4"><span class="section-number-4">3.3.1</span> Introduction</h4>
<div class="outline-text-4" id="text-3-3-1">
<p>
This section concerns API calls related to datasets.
@ -2479,8 +2479,8 @@ This section concerns API calls related to datasets.
</div>
</div>
<div id="outline-container-orgc6db6a8" class="outline-4">
<h4 id="orgc6db6a8"><span class="section-number-4">3.3.2</span> C templates for front end</h4>
<div id="outline-container-orgceee3cd" class="outline-4">
<h4 id="orgceee3cd"><span class="section-number-4">3.3.2</span> C templates for front end</h4>
<div class="outline-text-4" id="text-3-3-2">
<p>
The C templates that correspond to each of the abovementioned functions can be found below.
@ -2491,12 +2491,12 @@ The basic (non-suffixed) API call on datasets deals with double precision (see T
</p>
</div>
<div id="outline-container-org7dc8e91" class="outline-5">
<h5 id="org7dc8e91"><span class="section-number-5">3.3.2.1</span> Function declarations</h5>
<div id="outline-container-orgedf7b2b" class="outline-5">
<h5 id="orgedf7b2b"><span class="section-number-5">3.3.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-org28b3642" class="outline-5">
<h5 id="org28b3642"><span class="section-number-5">3.3.2.2</span> Source code for double precision functions</h5>
<div id="outline-container-org4686658" class="outline-5">
<h5 id="org4686658"><span class="section-number-5">3.3.2.2</span> Source code for double precision functions</h5>
<div class="outline-text-5" id="text-3-3-2-2">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -2659,8 +2659,8 @@ The basic (non-suffixed) API call on datasets deals with double precision (see T
</div>
</div>
<div id="outline-container-org4fb0ffc" class="outline-5">
<h5 id="org4fb0ffc"><span class="section-number-5">3.3.2.3</span> Source code for single precision functions</h5>
<div id="outline-container-orged99113" class="outline-5">
<h5 id="orged99113"><span class="section-number-5">3.3.2.3</span> Source code for single precision functions</h5>
<div class="outline-text-5" id="text-3-3-2-3">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -2811,11 +2811,11 @@ The basic (non-suffixed) API call on datasets deals with double precision (see T
</div>
</div>
<div id="outline-container-orgd506abb" class="outline-5">
<h5 id="orgd506abb"><span class="section-number-5">3.3.2.4</span> Source code for memory-safe functions</h5>
<div id="outline-container-orgecbbf28" class="outline-5">
<h5 id="orgecbbf28"><span class="section-number-5">3.3.2.4</span> Source code for memory-safe functions</h5>
<div class="outline-text-5" id="text-3-3-2-4">
<div class="org-src-container">
<pre class="src src-c" id="org99e70e0"><span style="color: #228b22;">trexio_exit_code</span> <span style="color: #a0522d;">rc</span>;
<pre class="src src-c" id="org3e97aa4"><span style="color: #228b22;">trexio_exit_code</span> <span style="color: #a0522d;">rc</span>;
int64_t $group_dset_dim$ = 0;
/* <span style="color: #b22222;">Error handling for this call is added by the generator </span>*/
@ -2971,8 +2971,8 @@ rc = trexio_read_$group_dset_dim$_64(file, &amp;($group_dset_dim$));
</div>
</div>
<div id="outline-container-orgc72a89f" class="outline-5">
<h5 id="orgc72a89f"><span class="section-number-5">3.3.2.5</span> Source code for default functions</h5>
<div id="outline-container-orgc3f84cd" class="outline-5">
<h5 id="orgc3f84cd"><span class="section-number-5">3.3.2.5</span> Source code for default functions</h5>
<div class="outline-text-5" id="text-3-3-2-5">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -3047,8 +3047,8 @@ rc = trexio_read_$group_dset_dim$_64(file, &amp;($group_dset_dim$));
</div>
</div>
<div id="outline-container-org637f67c" class="outline-4">
<h4 id="org637f67c"><span class="section-number-4">3.3.3</span> Fortran templates for front end</h4>
<div id="outline-container-orgfa99aae" class="outline-4">
<h4 id="orgfa99aae"><span class="section-number-4">3.3.3</span> Fortran templates for front end</h4>
<div class="outline-text-4" id="text-3-3-3">
<p>
The <code>Fortran</code> templates that provide an access to the <code>C</code> API calls from <code>Fortran</code>.
@ -3133,8 +3133,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-org71ac87c" class="outline-4">
<h4 id="org71ac87c"><span class="section-number-4">3.3.4</span> Python templates for front end</h4>
<div id="outline-container-org136cad8" class="outline-4">
<h4 id="org136cad8"><span class="section-number-4">3.3.4</span> Python templates for front end</h4>
<div class="outline-text-4" id="text-3-3-4">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">def</span> <span style="color: #0000ff;">write_</span>$group_dset$(trexio_file, dset_w) -&gt; <span style="color: #008b8b;">None</span>:
@ -3329,12 +3329,12 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-orgc8cbdc2" class="outline-3">
<h3 id="orgc8cbdc2"><span class="section-number-3">3.4</span> Templates for front end has/read/write a dataset of sparse data</h3>
<div id="outline-container-org6540cb5" class="outline-3">
<h3 id="org6540cb5"><span class="section-number-3">3.4</span> Templates for front end has/read/write a dataset of sparse data</h3>
<div class="outline-text-3" id="text-3-4">
</div>
<div id="outline-container-org2dbd6d8" class="outline-4">
<h4 id="org2dbd6d8"><span class="section-number-4">3.4.1</span> Introduction</h4>
<div id="outline-container-org2f58eed" class="outline-4">
<h4 id="org2f58eed"><span class="section-number-4">3.4.1</span> Introduction</h4>
<div class="outline-text-4" id="text-3-4-1">
<p>
Sparse data structures are used typically for large tensors such as
@ -3495,16 +3495,16 @@ This section concerns API calls related to sparse data structures.
</div>
</div>
<div id="outline-container-org3bb54f2" class="outline-4">
<h4 id="org3bb54f2"><span class="section-number-4">3.4.2</span> C templates for front end</h4>
<div id="outline-container-orgb32c4f0" class="outline-4">
<h4 id="orgb32c4f0"><span class="section-number-4">3.4.2</span> C templates for front end</h4>
<div class="outline-text-4" id="text-3-4-2">
</div>
<div id="outline-container-org3852d3e" class="outline-5">
<h5 id="org3852d3e"><span class="section-number-5">3.4.2.1</span> Function declarations</h5>
<div id="outline-container-orgec6d9b9" class="outline-5">
<h5 id="orgec6d9b9"><span class="section-number-5">3.4.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-org78a9a48" class="outline-5">
<h5 id="org78a9a48"><span class="section-number-5">3.4.2.2</span> Source code for default functions</h5>
<div id="outline-container-orga742e79" class="outline-5">
<h5 id="orga742e79"><span class="section-number-5">3.4.2.2</span> Source code for default functions</h5>
<div class="outline-text-5" id="text-3-4-2-2">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span> <span style="color: #0000ff;">trexio_read_safe_$group_dset$</span>(<span style="color: #228b22;">trexio_t</span>* <span style="color: #a020f0;">const</span> <span style="color: #a0522d;">file</span>,
@ -3779,8 +3779,8 @@ This section concerns API calls related to sparse data structures.
</div>
</div>
<div id="outline-container-org8d4827e" class="outline-4">
<h4 id="org8d4827e"><span class="section-number-4">3.4.3</span> Fortran templates for front end</h4>
<div id="outline-container-org8590459" class="outline-4">
<h4 id="org8590459"><span class="section-number-4">3.4.3</span> Fortran templates for front end</h4>
<div class="outline-text-4" id="text-3-4-3">
<p>
The <code>Fortran</code> templates that provide an access to the <code>C</code> API calls from <code>Fortran</code>.
@ -3875,8 +3875,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-org66e5208" class="outline-4">
<h4 id="org66e5208"><span class="section-number-4">3.4.4</span> Python templates for front end</h4>
<div id="outline-container-org4a68a2f" class="outline-4">
<h4 id="org4a68a2f"><span class="section-number-4">3.4.4</span> Python templates for front end</h4>
<div class="outline-text-4" id="text-3-4-4">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">def</span> <span style="color: #0000ff;">write_</span>$group_dset$(trexio_file: File, offset_file: <span style="color: #483d8b;">int</span>, buffer_size: <span style="color: #483d8b;">int</span>, indices: <span style="color: #483d8b;">list</span>, values: <span style="color: #483d8b;">list</span>) -&gt; <span style="color: #008b8b;">None</span>:
@ -4097,12 +4097,12 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-org5a110dd" class="outline-3">
<h3 id="org5a110dd"><span class="section-number-3">3.5</span> Templates for front end has/read/write a dataset of strings</h3>
<div id="outline-container-org88c4fb9" class="outline-3">
<h3 id="org88c4fb9"><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-org707985c" class="outline-4">
<h4 id="org707985c"><span class="section-number-4">3.5.1</span> Introduction</h4>
<div id="outline-container-org12c9e0b" class="outline-4">
<h4 id="org12c9e0b"><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.
@ -4142,8 +4142,8 @@ This section concerns API calls related to datasets of strings.
</div>
</div>
<div id="outline-container-org0bf2bdd" class="outline-4">
<h4 id="org0bf2bdd"><span class="section-number-4">3.5.2</span> C templates for front end</h4>
<div id="outline-container-orga05bc97" class="outline-4">
<h4 id="orga05bc97"><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
@ -4151,12 +4151,12 @@ to/from the <code>TREXIO</code> file (except for <code>trexio_has_</code> functi
</p>
</div>
<div id="outline-container-orgc2a964b" class="outline-5">
<h5 id="orgc2a964b"><span class="section-number-5">3.5.2.1</span> Function declarations</h5>
<div id="outline-container-org95700d6" class="outline-5">
<h5 id="org95700d6"><span class="section-number-5">3.5.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-orgc8b7ab8" class="outline-5">
<h5 id="orgc8b7ab8"><span class="section-number-5">3.5.2.2</span> Source code for default functions</h5>
<div id="outline-container-orgb137ac6" class="outline-5">
<h5 id="orgb137ac6"><span class="section-number-5">3.5.2.2</span> Source code for default functions</h5>
<div class="outline-text-5" id="text-3-5-2-2">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -4406,8 +4406,8 @@ to/from the <code>TREXIO</code> file (except for <code>trexio_has_</code> functi
</div>
</div>
<div id="outline-container-orga0d6452" class="outline-4">
<h4 id="orga0d6452"><span class="section-number-4">3.5.3</span> Fortran templates for front end</h4>
<div id="outline-container-orgfdbd72d" class="outline-4">
<h4 id="orgfdbd72d"><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>.
@ -4503,8 +4503,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-orgf5bdd7b" class="outline-4">
<h4 id="orgf5bdd7b"><span class="section-number-4">3.5.4</span> Python templates for front end</h4>
<div id="outline-container-orgb4947fc" class="outline-4">
<h4 id="orgb4947fc"><span class="section-number-4">3.5.4</span> Python templates for front end</h4>
<div class="outline-text-4" id="text-3-5-4">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">def</span> <span style="color: #0000ff;">write_</span>$group_dset$(trexio_file, dset_w: <span style="color: #483d8b;">list</span>) -&gt; <span style="color: #008b8b;">None</span>:
@ -4620,12 +4620,12 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-org7efbca8" class="outline-3">
<h3 id="org7efbca8"><span class="section-number-3">3.6</span> Templates for front end has/read/write a single string attribute</h3>
<div id="outline-container-orgbb467e6" class="outline-3">
<h3 id="orgbb467e6"><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-orgcc07c9c" class="outline-4">
<h4 id="orgcc07c9c"><span class="section-number-4">3.6.1</span> Introduction</h4>
<div id="outline-container-org5b1ba3b" class="outline-4">
<h4 id="org5b1ba3b"><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.
@ -4665,16 +4665,16 @@ This section concerns API calls related to string attributes.
</div>
</div>
<div id="outline-container-org84f0c73" class="outline-4">
<h4 id="org84f0c73"><span class="section-number-4">3.6.2</span> C templates for front end</h4>
<div id="outline-container-orgafa3aea" class="outline-4">
<h4 id="orgafa3aea"><span class="section-number-4">3.6.2</span> C templates for front end</h4>
<div class="outline-text-4" id="text-3-6-2">
</div>
<div id="outline-container-org62a6779" class="outline-5">
<h5 id="org62a6779"><span class="section-number-5">3.6.2.1</span> Function declarations</h5>
<div id="outline-container-org8611a9b" class="outline-5">
<h5 id="org8611a9b"><span class="section-number-5">3.6.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-orgee74d21" class="outline-5">
<h5 id="orgee74d21"><span class="section-number-5">3.6.2.2</span> Source code for default functions</h5>
<div id="outline-container-orgf159f96" class="outline-5">
<h5 id="orgf159f96"><span class="section-number-5">3.6.2.2</span> Source code for default functions</h5>
<div class="outline-text-5" id="text-3-6-2-2">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -4778,8 +4778,8 @@ This section concerns API calls related to string attributes.
</div>
</div>
<div id="outline-container-org381b62d" class="outline-4">
<h4 id="org381b62d"><span class="section-number-4">3.6.3</span> Fortran templates for front end</h4>
<div id="outline-container-orgc7a4f33" class="outline-4">
<h4 id="orgc7a4f33"><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.
@ -4856,8 +4856,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-org92b4376" class="outline-4">
<h4 id="org92b4376"><span class="section-number-4">3.6.4</span> Python templates for front end</h4>
<div id="outline-container-orga258076" class="outline-4">
<h4 id="orga258076"><span class="section-number-4">3.6.4</span> Python templates for front end</h4>
<div class="outline-text-4" id="text-3-6-4">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">def</span> <span style="color: #0000ff;">write_</span>$group_str$(trexio_file, str_w: <span style="color: #483d8b;">str</span>) -&gt; <span style="color: #008b8b;">None</span>:
@ -4947,8 +4947,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-org37cddcc" class="outline-2">
<h2 id="org37cddcc"><span class="section-number-2">4</span> Fortran helper/wrapper functions</h2>
<div id="outline-container-orgfd9b6ad" class="outline-2">
<h2 id="orgfd9b6ad"><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.
@ -5083,7 +5083,7 @@ 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: 2022-01-13 Thu 12:27</p>
<p class="date">Created: 2022-01-17 Mon 18:15</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

64
templator_hdf5.html
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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-01-13 Thu 12:27 -->
<!-- 2022-01-17 Mon 18:15 -->
<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>
@ -311,29 +311,29 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org3bc92a7">1. HDF5 back end</a>
<li><a href="#org3966719">1. HDF5 back end</a>
<ul>
<li><a href="#orgb0abf9e">1.1. Template for HDF5 definitions</a></li>
<li><a href="#org35cce14">1.2. Template for HDF5 structures</a></li>
<li><a href="#orgd2d0712">1.3. Template for HDF5 init/deinit</a></li>
<li><a href="#org06c4756">1.4. Template for HDF5 has/read/write the numerical attribute</a></li>
<li><a href="#orgfa241c5">1.5. Template for HDF5 has/read/write the dataset of numerical data</a></li>
<li><a href="#org701bae6">1.6. Template for HDF5 has/read/write the dataset of sparse data</a></li>
<li><a href="#orgb5f34d8">1.7. Template for HDF5 has/read/write the dataset of strings</a></li>
<li><a href="#orgb9ff710">1.8. Template for HDF5 has/read/write the string attribute</a></li>
<li><a href="#org58274bd">1.9. Helper functions</a></li>
<li><a href="#orgb4cea03">1.1. Template for HDF5 definitions</a></li>
<li><a href="#orgbfa94e1">1.2. Template for HDF5 structures</a></li>
<li><a href="#orgabc2887">1.3. Template for HDF5 init/deinit</a></li>
<li><a href="#org4fd2221">1.4. Template for HDF5 has/read/write the numerical attribute</a></li>
<li><a href="#orgf87e32d">1.5. Template for HDF5 has/read/write the dataset of numerical data</a></li>
<li><a href="#org334aa83">1.6. Template for HDF5 has/read/write the dataset of sparse data</a></li>
<li><a href="#org1e41326">1.7. Template for HDF5 has/read/write the dataset of strings</a></li>
<li><a href="#org3cc6816">1.8. Template for HDF5 has/read/write the string attribute</a></li>
<li><a href="#orgfbded59">1.9. Helper functions</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org3bc92a7" class="outline-2">
<h2 id="org3bc92a7"><span class="section-number-2">1</span> HDF5 back end</h2>
<div id="outline-container-org3966719" class="outline-2">
<h2 id="org3966719"><span class="section-number-2">1</span> HDF5 back end</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-orgb0abf9e" class="outline-3">
<h3 id="orgb0abf9e"><span class="section-number-3">1.1</span> Template for HDF5 definitions</h3>
<div id="outline-container-orgb4cea03" class="outline-3">
<h3 id="orgb4cea03"><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>
@ -345,8 +345,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org35cce14" class="outline-3">
<h3 id="org35cce14"><span class="section-number-3">1.2</span> Template for HDF5 structures</h3>
<div id="outline-container-orgbfa94e1" class="outline-3">
<h3 id="orgbfa94e1"><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> {
@ -360,8 +360,8 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-orgd2d0712" class="outline-3">
<h3 id="orgd2d0712"><span class="section-number-3">1.3</span> Template for HDF5 init/deinit</h3>
<div id="outline-container-orgabc2887" class="outline-3">
<h3 id="orgabc2887"><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>
@ -441,8 +441,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org06c4756" class="outline-3">
<h3 id="org06c4756"><span class="section-number-3">1.4</span> Template for HDF5 has/read/write the numerical attribute</h3>
<div id="outline-container-org4fd2221" class="outline-3">
<h3 id="org4fd2221"><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>
@ -536,8 +536,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-orgfa241c5" class="outline-3">
<h3 id="orgfa241c5"><span class="section-number-3">1.5</span> Template for HDF5 has/read/write the dataset of numerical data</h3>
<div id="outline-container-orgf87e32d" class="outline-3">
<h3 id="orgf87e32d"><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>
@ -659,8 +659,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org701bae6" class="outline-3">
<h3 id="org701bae6"><span class="section-number-3">1.6</span> Template for HDF5 has/read/write the dataset of sparse data</h3>
<div id="outline-container-org334aa83" class="outline-3">
<h3 id="org334aa83"><span class="section-number-3">1.6</span> Template for HDF5 has/read/write the dataset of sparse data</h3>
<div class="outline-text-3" id="text-1-6">
<p>
Sparse data is stored using extensible datasets of HDF5. Extensibility is required
@ -861,8 +861,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-orgb5f34d8" class="outline-3">
<h3 id="orgb5f34d8"><span class="section-number-3">1.7</span> Template for HDF5 has/read/write the dataset of strings</h3>
<div id="outline-container-org1e41326" class="outline-3">
<h3 id="org1e41326"><span class="section-number-3">1.7</span> Template for HDF5 has/read/write the dataset of strings</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>
@ -1066,8 +1066,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-orgb9ff710" class="outline-3">
<h3 id="orgb9ff710"><span class="section-number-3">1.8</span> Template for HDF5 has/read/write the string attribute</h3>
<div id="outline-container-org3cc6816" class="outline-3">
<h3 id="org3cc6816"><span class="section-number-3">1.8</span> Template for HDF5 has/read/write the string 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>
@ -1189,8 +1189,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
</div>
<div id="outline-container-org58274bd" class="outline-3">
<h3 id="org58274bd"><span class="section-number-3">1.9</span> Helper functions</h3>
<div id="outline-container-orgfbded59" class="outline-3">
<h3 id="orgfbded59"><span class="section-number-3">1.9</span> Helper functions</h3>
<div class="outline-text-3" id="text-1-9">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1452,7 +1452,7 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-01-13 Thu 12:27</p>
<p class="date">Created: 2022-01-17 Mon 18:15</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

82
templator_text.html
View File

@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-01-13 Thu 12:27 -->
<!-- 2022-01-17 Mon 18:15 -->
<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>
@ -311,28 +311,28 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgd712394">1. TEXT back end</a>
<li><a href="#org0728860">1. TEXT back end</a>
<ul>
<li><a href="#org2796502">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#org9ce43d3">1.2. Template for general structure in text back end</a></li>
<li><a href="#org2b0fe6b">1.3. Initialize function (constant part)</a></li>
<li><a href="#org493fa6d">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#org1d2dbbd">1.5. Template for text read struct</a></li>
<li><a href="#org59827c6">1.6. Template for text flush struct</a></li>
<li><a href="#org8578be9">1.7. Template for text free memory</a></li>
<li><a href="#org45d5014">1.8. Template for has/read/write the numerical attribute</a></li>
<li><a href="#orgc8400aa">1.9. Template for has/read/write the dataset of numerical data</a></li>
<li><a href="#org941e3d5">1.10. Template for has/read/write the dataset of strings</a></li>
<li><a href="#org10c5226">1.11. Template for has/read/write the string attribute</a></li>
<li><a href="#orga9458aa">1.12. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orgca864f4">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#org193aeba">1.2. Template for general structure in text back end</a></li>
<li><a href="#org772ba16">1.3. Initialize function (constant part)</a></li>
<li><a href="#org764b1fd">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#org3b0d3ec">1.5. Template for text read struct</a></li>
<li><a href="#orga1e0ffc">1.6. Template for text flush struct</a></li>
<li><a href="#orgf719c57">1.7. Template for text free memory</a></li>
<li><a href="#org3603e92">1.8. Template for has/read/write the numerical attribute</a></li>
<li><a href="#orgab74cab">1.9. Template for has/read/write the dataset of numerical data</a></li>
<li><a href="#org3aed1f9">1.10. Template for has/read/write the dataset of strings</a></li>
<li><a href="#org4630648">1.11. Template for has/read/write the string attribute</a></li>
<li><a href="#orgdff8e78">1.12. Template for has/read/write the dataset of sparse data</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-orgd712394" class="outline-2">
<h2 id="orgd712394"><span class="section-number-2">1</span> TEXT back end</h2>
<div id="outline-container-org0728860" class="outline-2">
<h2 id="org0728860"><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
@ -353,8 +353,8 @@ The file is written when closed, or when the flush function is called.
</p>
</div>
<div id="outline-container-org2796502" class="outline-3">
<h3 id="org2796502"><span class="section-number-3">1.1</span> Template for group-related structures in text back end</h3>
<div id="outline-container-orgca864f4" class="outline-3">
<h3 id="orgca864f4"><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 {
@ -373,8 +373,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-org9ce43d3" class="outline-3">
<h3 id="org9ce43d3"><span class="section-number-3">1.2</span> Template for general structure in text back end</h3>
<div id="outline-container-org193aeba" class="outline-3">
<h3 id="org193aeba"><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;">trexio_text_s</span> {
@ -387,8 +387,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-org2b0fe6b" class="outline-3">
<h3 id="org2b0fe6b"><span class="section-number-3">1.3</span> Initialize function (constant part)</h3>
<div id="outline-container-org772ba16" class="outline-3">
<h3 id="org772ba16"><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>
@ -519,8 +519,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-org493fa6d" class="outline-3">
<h3 id="org493fa6d"><span class="section-number-3">1.4</span> Deinitialize function (templated part)</h3>
<div id="outline-container-org764b1fd" class="outline-3">
<h3 id="org764b1fd"><span class="section-number-3">1.4</span> Deinitialize function (templated part)</h3>
<div class="outline-text-3" id="text-1-4">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -542,8 +542,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-org1d2dbbd" class="outline-3">
<h3 id="org1d2dbbd"><span class="section-number-3">1.5</span> Template for text read struct</h3>
<div id="outline-container-org3b0d3ec" class="outline-3">
<h3 id="org3b0d3ec"><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*
@ -835,8 +835,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org59827c6" class="outline-3">
<h3 id="org59827c6"><span class="section-number-3">1.6</span> Template for text flush struct</h3>
<div id="outline-container-orga1e0ffc" class="outline-3">
<h3 id="orga1e0ffc"><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>
@ -901,8 +901,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org8578be9" class="outline-3">
<h3 id="org8578be9"><span class="section-number-3">1.7</span> Template for text free memory</h3>
<div id="outline-container-orgf719c57" class="outline-3">
<h3 id="orgf719c57"><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.
@ -947,8 +947,8 @@ Memory is allocated when reading. The following function frees memory.
</div>
</div>
<div id="outline-container-org45d5014" class="outline-3">
<h3 id="org45d5014"><span class="section-number-3">1.8</span> Template for has/read/write the numerical attribute</h3>
<div id="outline-container-org3603e92" class="outline-3">
<h3 id="org3603e92"><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>
@ -1011,8 +1011,8 @@ Memory is allocated when reading. The following function frees memory.
</div>
</div>
<div id="outline-container-orgc8400aa" class="outline-3">
<h3 id="orgc8400aa"><span class="section-number-3">1.9</span> Template for has/read/write the dataset of numerical data</h3>
<div id="outline-container-orgab74cab" class="outline-3">
<h3 id="orgab74cab"><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.
@ -1108,8 +1108,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org941e3d5" class="outline-3">
<h3 id="org941e3d5"><span class="section-number-3">1.10</span> Template for has/read/write the dataset of strings</h3>
<div id="outline-container-org3aed1f9" class="outline-3">
<h3 id="org3aed1f9"><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.
@ -1210,8 +1210,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org10c5226" class="outline-3">
<h3 id="org10c5226"><span class="section-number-3">1.11</span> Template for has/read/write the string attribute</h3>
<div id="outline-container-org4630648" class="outline-3">
<h3 id="org4630648"><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>
@ -1285,8 +1285,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orga9458aa" class="outline-3">
<h3 id="orga9458aa"><span class="section-number-3">1.12</span> Template for has/read/write the dataset of sparse data</h3>
<div id="outline-container-orgdff8e78" class="outline-3">
<h3 id="orgdff8e78"><span class="section-number-3">1.12</span> Template for has/read/write the dataset of sparse data</h3>
<div class="outline-text-3" id="text-1-12">
<p>
Each sparse array is stored in a separate <code>.txt</code> file due to the fact that sparse I/O has to be decoupled
@ -1563,7 +1563,7 @@ User provides indices and values of the sparse array as two separate variables.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-01-13 Thu 12:27</p>
<p class="date">Created: 2022-01-17 Mon 18:15</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>
<!-- 2022-01-13 Thu 12:27 -->
<!-- 2022-01-17 Mon 18:16 -->
<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="#org607846c">1. Metadata (metadata group)</a></li>
<li><a href="#org8f5e27d">2. Electron (electron group)</a></li>
<li><a href="#org774d087">3. Nucleus (nucleus group)</a></li>
<li><a href="#org41dadda">4. Effective core potentials (ecp group)</a>
<li><a href="#org75f87e8">1. Metadata (metadata group)</a></li>
<li><a href="#orgbe9dae4">2. Electron (electron group)</a></li>
<li><a href="#org620cd51">3. Nucleus (nucleus group)</a></li>
<li><a href="#orgc153f72">4. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org3a05dab">4.1. Example</a></li>
<li><a href="#org545e12b">4.1. Example</a></li>
</ul>
</li>
<li><a href="#org61a6d52">5. Basis set (basis group)</a>
<li><a href="#orgd447554">5. Basis set (basis group)</a>
<ul>
<li><a href="#org7459d15">5.1. Example</a></li>
<li><a href="#org933e3ee">5.1. Example</a></li>
</ul>
</li>
<li><a href="#org92e67b0">6. Atomic orbitals (ao group)</a>
<li><a href="#orgab737e0">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="#org7c9c90b">7. Molecular orbitals (mo group)</a>
<li><a href="#org8cc55bf">7. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org64e96d0">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org9a813a7">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org8113b6b">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgefc0cea">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#orgcf907e7">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#org83dcc2c">9. Reduced density matrices (rdm group)</a></li>
<li><a href="#orgf0ed2d5">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#orgfca3754">9. Reduced density matrices (rdm group)</a></li>
</ul>
</div>
</div>
@ -409,8 +409,8 @@ fetched using multiple function calls to perform I/O on buffers.
</p>
<div id="outline-container-org607846c" class="outline-2">
<h2 id="org607846c"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org75f87e8" class="outline-2">
<h2 id="org75f87e8"><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
@ -420,7 +420,7 @@ which have participated to the creation of the file, a list of
authors of the file, and a textual description.
</p>
<table id="orgd29fd5c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org1576189" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -487,15 +487,15 @@ authors of the file, and a textual description.
</div>
</div>
<div id="outline-container-org8f5e27d" class="outline-2">
<h2 id="org8f5e27d"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div id="outline-container-orgbe9dae4" class="outline-2">
<h2 id="orgbe9dae4"><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="org2225bca" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org0d492f2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -534,15 +534,15 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-org774d087" class="outline-2">
<h2 id="org774d087"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div id="outline-container-org620cd51" class="outline-2">
<h2 id="org620cd51"><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="org70ef21a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgaed0075" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -609,8 +609,8 @@ given in Cartesian \((x,y,z)\) format.
</div>
</div>
<div id="outline-container-org41dadda" class="outline-2">
<h2 id="org41dadda"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div id="outline-container-orgc153f72" class="outline-2">
<h2 id="orgc153f72"><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
@ -643,7 +643,7 @@ 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="orgc981541" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org8ad6585" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -741,8 +741,8 @@ The latter causes issues when written before <code>ang_mom</code> in the TREXIO
</p>
</div>
<div id="outline-container-org3a05dab" class="outline-3">
<h3 id="org3a05dab"><span class="section-number-3">4.1</span> Example</h3>
<div id="outline-container-org545e12b" class="outline-3">
<h3 id="org545e12b"><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
@ -805,8 +805,8 @@ power = [
</div>
</div>
<div id="outline-container-org61a6d52" class="outline-2">
<h2 id="org61a6d52"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div id="outline-container-orgd447554" class="outline-2">
<h2 id="orgd447554"><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
@ -859,7 +859,7 @@ 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="org2aa4601" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf1b00b2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -953,8 +953,8 @@ All the basis set parameters are stored in one-dimensional arrays:
</table>
</div>
<div id="outline-container-org7459d15" class="outline-3">
<h3 id="org7459d15"><span class="section-number-3">5.1</span> Example</h3>
<div id="outline-container-org933e3ee" class="outline-3">
<h3 id="org933e3ee"><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
@ -1032,8 +1032,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-org92e67b0" class="outline-2">
<h2 id="org92e67b0"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div id="outline-container-orgab737e0" class="outline-2">
<h2 id="orgab737e0"><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
@ -1085,13 +1085,13 @@ shell, as in the GAMESS convention where
<p>
In such a case, one should set the normalization of the shell (in
the <a href="#org61a6d52">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#orgd447554">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="org33dc11a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org9b679f4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1143,8 +1143,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
</table>
</div>
<div id="outline-container-orgd8d1afe" class="outline-3">
<h3 id="ao_one_e"><a id="orgd8d1afe"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div id="outline-container-org08cb618" class="outline-3">
<h3 id="ao_one_e"><a id="org08cb618"></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}}
@ -1162,7 +1162,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="org5156a4e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org18971b6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1229,8 +1229,8 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org2b0f127" class="outline-3">
<h3 id="ao_two_e"><a id="org2b0f127"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div id="outline-container-orge73fb15" class="outline-3">
<h3 id="ao_two_e"><a id="orge73fb15"></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
@ -1251,7 +1251,7 @@ notation.
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
</ul>
<table id="org9fa2d0a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge666d13" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1291,10 +1291,10 @@ notation.
</div>
</div>
<div id="outline-container-org7c9c90b" class="outline-2">
<h2 id="org7c9c90b"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div id="outline-container-org8cc55bf" class="outline-2">
<h2 id="org8cc55bf"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div class="outline-text-2" id="text-7">
<table id="orgf9f1908" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc125343" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1360,8 +1360,8 @@ notation.
</table>
</div>
<div id="outline-container-org64e96d0" class="outline-3">
<h3 id="org64e96d0"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div id="outline-container-org8113b6b" class="outline-3">
<h3 id="org8113b6b"><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
@ -1369,7 +1369,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="orgb9a93f5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2a44911" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1436,8 +1436,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org9a813a7" class="outline-3">
<h3 id="org9a813a7"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div id="outline-container-orgefc0cea" class="outline-3">
<h3 id="orgefc0cea"><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
@ -1445,7 +1445,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="orgdecd1cc" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org29aa490" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1485,11 +1485,11 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-orgcf907e7" class="outline-2">
<h2 id="orgcf907e7"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
<div id="outline-container-orgf0ed2d5" class="outline-2">
<h2 id="orgf0ed2d5"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
</div>
<div id="outline-container-org83dcc2c" class="outline-2">
<h2 id="org83dcc2c"><span class="section-number-2">9</span> Reduced density matrices (rdm group)</h2>
<div id="outline-container-orgfca3754" class="outline-2">
<h2 id="orgfca3754"><span class="section-number-2">9</span> Reduced density matrices (rdm group)</h2>
<div class="outline-text-2" id="text-9">
<p>
The reduced density matrices are defined in the basis of molecular
@ -1542,7 +1542,7 @@ The total energy can be computed as:
\]
</p>
<table id="org0c81fdb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf5bd757" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1625,7 +1625,7 @@ The total energy can be computed as:
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-01-13 Thu 12:27</p>
<p class="date">Created: 2022-01-17 Mon 18:16</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>