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README.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-01-07 Fri 10:59 -->
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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" />
<meta name=google-site-verification content=jdDnuP2rYGJVy8AHSd-8LkmOmvK_dyz5buZ98wilYII />
@ -348,7 +348,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-01-07 Fri 10:59</p>
<p class="date">Created: 2022-01-07 Fri 14:38</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<head>
<!-- 2022-01-07 Fri 10:59 -->
<!-- 2022-01-07 Fri 14:38 -->
<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="#orgfd161ff">1. Accessing sparse quantities</a>
<li><a href="#orgddad97b">1. Accessing sparse quantities</a>
<ul>
<li><a href="#org3f9ee2d">1.1. Fortran</a>
<li><a href="#org90a0fa6">1.1. Fortran</a>
<ul>
<li><a href="#orgbc33e4a">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org2907677">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org8db445c">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org7153425">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org949f3ac">1.1.5. Allocate memory</a></li>
<li><a href="#org18a6066">1.1.6. Read one-electron quantities</a></li>
<li><a href="#orgdf7d111">1.1.7. Read two-electron quantities</a>
<li><a href="#orgc3057b0">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org945f18f">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org564e54a">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org201ea57">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org3ff57dc">1.1.5. Allocate memory</a></li>
<li><a href="#orgfdd2452">1.1.6. Read one-electron quantities</a></li>
<li><a href="#org952b4a0">1.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org013932b">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org0abcf69">1.1.7.2. Reduced density matrix</a></li>
<li><a href="#org771ce7f">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org214daf2">1.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org2812854">1.1.8. Compute the energy</a></li>
<li><a href="#org13f38d4">1.1.9. Terminate</a></li>
<li><a href="#org68255a1">1.1.8. Compute the energy</a></li>
<li><a href="#orgbe30ee3">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-orgfd161ff" class="outline-2">
<h2 id="orgfd161ff"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
<div id="outline-container-orgddad97b" class="outline-2">
<h2 id="orgddad97b"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-org3f9ee2d" class="outline-3">
<h3 id="org3f9ee2d"><span class="section-number-3">1.1</span> Fortran</h3>
<div id="outline-container-org90a0fa6" class="outline-3">
<h3 id="org90a0fa6"><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>
@ -413,8 +413,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-orgbc33e4a" class="outline-4">
<h4 id="orgbc33e4a"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-orgc3057b0" class="outline-4">
<h4 id="orgc3057b0"><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>
@ -429,8 +429,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org2907677" class="outline-4">
<h4 id="org2907677"><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-org945f18f" class="outline-4">
<h4 id="org945f18f"><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)
@ -446,8 +446,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-org8db445c" class="outline-4">
<h4 id="org8db445c"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org564e54a" class="outline-4">
<h4 id="org564e54a"><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)
@ -461,8 +461,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-org7153425" class="outline-4">
<h4 id="org7153425"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org201ea57" class="outline-4">
<h4 id="org201ea57"><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)
@ -476,8 +476,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-org949f3ac" class="outline-4">
<h4 id="org949f3ac"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div id="outline-container-org3ff57dc" class="outline-4">
<h4 id="org3ff57dc"><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) )
@ -489,8 +489,8 @@ W(:,:,:,:) = 0.d0
</div>
</div>
<div id="outline-container-org18a6066" class="outline-4">
<h4 id="org18a6066"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-orgfdd2452" class="outline-4">
<h4 id="orgfdd2452"><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)
@ -522,8 +522,8 @@ rc = trexio_read_rdm_1e(f, D)
</div>
</div>
<div id="outline-container-orgdf7d111" class="outline-4">
<h4 id="orgdf7d111"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-org952b4a0" class="outline-4">
<h4 id="org952b4a0"><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
@ -539,8 +539,8 @@ to be protected in the critical section when modified.
</p>
</div>
<div id="outline-container-org013932b" class="outline-5">
<h5 id="org013932b"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org771ce7f" class="outline-5">
<h5 id="org771ce7f"><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)
@ -589,8 +589,8 @@ icount = BUFSIZE
</div>
</div>
<div id="outline-container-org0abcf69" class="outline-5">
<h5 id="org0abcf69"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org214daf2" class="outline-5">
<h5 id="org214daf2"><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)
@ -634,8 +634,8 @@ icount = bufsize
</div>
</div>
<div id="outline-container-org2812854" class="outline-4">
<h4 id="org2812854"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div id="outline-container-org68255a1" class="outline-4">
<h4 id="org68255a1"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div class="outline-text-4" id="text-1-1-8">
<p>
As \((n,m)\) 2D arrays are stored in memory as \((\n times m)\) 1D
@ -669,8 +669,8 @@ E = E + E_nn
</div>
</div>
<div id="outline-container-org13f38d4" class="outline-4">
<h4 id="org13f38d4"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div id="outline-container-orgbe30ee3" class="outline-4">
<h4 id="orgbe30ee3"><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 )
@ -685,7 +685,7 @@ E = E + E_nn
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-01-07 Fri 10:59</p>
<p class="date">Created: 2022-01-07 Fri 14:38</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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index.html
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-01-07 Fri 10:59 -->
<!-- 2022-01-07 Fri 14:38 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name=google-site-verification content=jdDnuP2rYGJVy8AHSd-8LkmOmvK_dyz5buZ98wilYII />
@ -348,7 +348,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-01-07 Fri 10:59</p>
<p class="date">Created: 2022-01-07 Fri 14:38</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>
<!-- 2022-01-07 Fri 10:59 -->
<!-- 2022-01-07 Fri 14:38 -->
<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="#org1f42dad">1. Coding conventions</a>
<li><a href="#org13099ac">1. Coding conventions</a>
<ul>
<li><a href="#org420d6c1">1.1. Memory allocation</a></li>
<li><a href="#org34ad392">1.1. Memory allocation</a></li>
</ul>
</li>
<li><a href="#orgcdf88c5">2. Front end</a>
<li><a href="#org89e6683">2. Front end</a>
<ul>
<li><a href="#orgbd8029a">2.1. Error handling</a>
<li><a href="#orged21c99">2.1. Error handling</a>
<ul>
<li><a href="#org6d2dd1c">2.1.1. Decoding errors</a>
<li><a href="#org3429912">2.1.1. Decoding errors</a>
<ul>
<li><a href="#orgac101b8">2.1.1.1. C source code</a></li>
<li><a href="#orgf143850">2.1.1.2. Fortran interface</a></li>
<li><a href="#org0138108">2.1.1.3. Python interface</a></li>
<li><a href="#org30faad5">2.1.1.1. C source code</a></li>
<li><a href="#org9f0a40e">2.1.1.2. Fortran interface</a></li>
<li><a href="#org2975392">2.1.1.3. Python interface</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgde370e3">2.2. Back ends</a>
<li><a href="#org7bab42c">2.2. Back ends</a>
<ul>
<li><a href="#org59064d4">2.2.1. C</a></li>
<li><a href="#orga6dd3b9">2.2.2. Fortran</a></li>
<li><a href="#orgde9eaac">2.2.3. Python</a></li>
<li><a href="#org95b723d">2.2.1. C</a></li>
<li><a href="#org5f9f84d">2.2.2. Fortran</a></li>
<li><a href="#org093eff1">2.2.3. Python</a></li>
</ul>
</li>
<li><a href="#org005582c">2.3. Read/write behavior</a></li>
<li><a href="#org54159a7">2.4. TREXIO file type</a>
<li><a href="#org03ea95b">2.3. Read/write behavior</a></li>
<li><a href="#org9fd6ba6">2.4. TREXIO file type</a>
<ul>
<li><a href="#org5c2b930">2.4.1. TREXIO<sub>File</sub> Python class</a></li>
<li><a href="#org29f9ece">2.4.1. TREXIO<sub>File</sub> Python class</a></li>
</ul>
</li>
<li><a href="#org5f408da">2.5. Polymorphism of the file handle</a></li>
<li><a href="#orgf2b055a">2.6. File opening</a>
<li><a href="#org2b10759">2.5. Polymorphism of the file handle</a></li>
<li><a href="#orgd8a709a">2.6. File opening</a>
<ul>
<li><a href="#org777a8c9">2.6.1. C</a></li>
<li><a href="#orga4e2136">2.6.2. Fortran</a></li>
<li><a href="#org17026c9">2.6.3. Python</a></li>
<li><a href="#orgb6f8fa7">2.6.4. Zero-based versus one-based arrays of indices</a></li>
<li><a href="#org7e04aa1">2.6.1. C</a></li>
<li><a href="#org9f61088">2.6.2. Fortran</a></li>
<li><a href="#org4f5d14b">2.6.3. Python</a></li>
<li><a href="#org3e354ce">2.6.4. Zero-based versus one-based arrays of indices</a></li>
</ul>
</li>
<li><a href="#org54fb930">2.7. File closing</a>
<li><a href="#orgfc04ec5">2.7. File closing</a>
<ul>
<li><a href="#orgcfd2c85">2.7.1. C</a></li>
<li><a href="#org33208a4">2.7.2. Fortran</a></li>
<li><a href="#orgeb04f63">2.7.3. Python</a></li>
<li><a href="#orgdd511cc">2.7.1. C</a></li>
<li><a href="#org67bd30a">2.7.2. Fortran</a></li>
<li><a href="#orgf5fce4c">2.7.3. Python</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgb6be22b">3. Templates for front end</a>
<li><a href="#orgc6de66c">3. Templates for front end</a>
<ul>
<li><a href="#orgb46c957">3.1. Description</a></li>
<li><a href="#org18db8d1">3.2. Templates for front end has/read/write a single numerical attribute</a>
<li><a href="#org5b79f78">3.1. Description</a></li>
<li><a href="#org16cc9b6">3.2. Templates for front end has/read/write a single numerical attribute</a>
<ul>
<li><a href="#org93b71c6">3.2.1. Introduction</a></li>
<li><a href="#orgfa7f415">3.2.2. C templates for front end</a>
<li><a href="#orgcdb736c">3.2.1. Introduction</a></li>
<li><a href="#org1af320d">3.2.2. C templates for front end</a>
<ul>
<li><a href="#org4e07a06">3.2.2.1. Function declarations</a></li>
<li><a href="#org6539816">3.2.2.2. Source code for double precision functions</a></li>
<li><a href="#orga8ad191">3.2.2.3. Source code for single precision functions</a></li>
<li><a href="#orga47df8b">3.2.2.4. Source code for default functions</a></li>
<li><a href="#orgc65667e">3.2.2.1. Function declarations</a></li>
<li><a href="#org35bf507">3.2.2.2. Source code for double precision functions</a></li>
<li><a href="#org159f0f2">3.2.2.3. Source code for single precision functions</a></li>
<li><a href="#org9c08355">3.2.2.4. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#orgc1008e0">3.2.3. Fortran templates for front end</a></li>
<li><a href="#org734b154">3.2.4. Python templates for front end</a></li>
<li><a href="#org6b45a2b">3.2.3. Fortran templates for front end</a></li>
<li><a href="#orga220a91">3.2.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#org0607313">3.3. Templates for front end has/read/write a dataset of numerical data</a>
<li><a href="#org9e280b5">3.3. Templates for front end has/read/write a dataset of numerical data</a>
<ul>
<li><a href="#org24dff52">3.3.1. Introduction</a></li>
<li><a href="#org233bbeb">3.3.2. C templates for front end</a>
<li><a href="#org3e4c230">3.3.1. Introduction</a></li>
<li><a href="#org884b9d3">3.3.2. C templates for front end</a>
<ul>
<li><a href="#org0a85166">3.3.2.1. Function declarations</a></li>
<li><a href="#orgc5b2327">3.3.2.2. Source code for double precision functions</a></li>
<li><a href="#orgcd80c5c">3.3.2.3. Source code for single precision functions</a></li>
<li><a href="#org316ada3">3.3.2.4. Source code for memory-safe functions</a></li>
<li><a href="#org07ea3b3">3.3.2.5. Source code for default functions</a></li>
<li><a href="#org0f50274">3.3.2.1. Function declarations</a></li>
<li><a href="#org11bf6d1">3.3.2.2. Source code for double precision functions</a></li>
<li><a href="#orgd305652">3.3.2.3. Source code for single precision functions</a></li>
<li><a href="#org608a8ed">3.3.2.4. Source code for memory-safe functions</a></li>
<li><a href="#orgcbb3bc6">3.3.2.5. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#org3222f78">3.3.3. Fortran templates for front end</a></li>
<li><a href="#orgb733819">3.3.4. Python templates for front end</a></li>
<li><a href="#org0221e05">3.3.3. Fortran templates for front end</a></li>
<li><a href="#org62c9c2a">3.3.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#org064c06b">3.4. Templates for front end has/read/write a dataset of sparse data</a>
<li><a href="#org9d5d85f">3.4. Templates for front end has/read/write a dataset of sparse data</a>
<ul>
<li><a href="#org1ea1e70">3.4.1. Introduction</a></li>
<li><a href="#orge3a9eec">3.4.2. C templates for front end</a>
<li><a href="#org571739f">3.4.1. Introduction</a></li>
<li><a href="#org3df96b6">3.4.2. C templates for front end</a>
<ul>
<li><a href="#org518c6f8">3.4.2.1. Function declarations</a></li>
<li><a href="#orgd9ecf4a">3.4.2.2. Source code for default functions</a></li>
<li><a href="#orgf089ef4">3.4.2.1. Function declarations</a></li>
<li><a href="#org5311b1f">3.4.2.2. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#org45e6cef">3.4.3. Fortran templates for front end</a></li>
<li><a href="#orga7e7aa3">3.4.4. Python templates for front end</a></li>
<li><a href="#org7c5f899">3.4.3. Fortran templates for front end</a></li>
<li><a href="#orgcd49ca5">3.4.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#orge55d6c1">3.5. Templates for front end has/read/write a dataset of strings</a>
<li><a href="#org4f02b0d">3.5. Templates for front end has/read/write a dataset of strings</a>
<ul>
<li><a href="#orgb0ad180">3.5.1. Introduction</a></li>
<li><a href="#org98d39aa">3.5.2. C templates for front end</a>
<li><a href="#org2901aa7">3.5.1. Introduction</a></li>
<li><a href="#orge9261ad">3.5.2. C templates for front end</a>
<ul>
<li><a href="#org37a0752">3.5.2.1. Function declarations</a></li>
<li><a href="#orgdfe738e">3.5.2.2. Source code for default functions</a></li>
<li><a href="#org3e59e01">3.5.2.1. Function declarations</a></li>
<li><a href="#orgac2d1a4">3.5.2.2. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#org3ebd5f9">3.5.3. Fortran templates for front end</a></li>
<li><a href="#org19b4d9e">3.5.4. Python templates for front end</a></li>
<li><a href="#orgee973ae">3.5.3. Fortran templates for front end</a></li>
<li><a href="#orgfc92d4f">3.5.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#org825ed85">3.6. Templates for front end has/read/write a single string attribute</a>
<li><a href="#orge1b0164">3.6. Templates for front end has/read/write a single string attribute</a>
<ul>
<li><a href="#org970347a">3.6.1. Introduction</a></li>
<li><a href="#orgdd5cf69">3.6.2. C templates for front end</a>
<li><a href="#orgdd4d354">3.6.1. Introduction</a></li>
<li><a href="#org183de38">3.6.2. C templates for front end</a>
<ul>
<li><a href="#org47b3e25">3.6.2.1. Function declarations</a></li>
<li><a href="#org0acd87e">3.6.2.2. Source code for default functions</a></li>
<li><a href="#orga50be4c">3.6.2.1. Function declarations</a></li>
<li><a href="#org5901247">3.6.2.2. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#org37e265f">3.6.3. Fortran templates for front end</a></li>
<li><a href="#orgaf1b596">3.6.4. Python templates for front end</a></li>
<li><a href="#orge63b532">3.6.3. Fortran templates for front end</a></li>
<li><a href="#org36313bf">3.6.4. Python templates for front end</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org24d66f7">4. Fortran helper/wrapper functions</a></li>
<li><a href="#orgec52913">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-org1f42dad" class="outline-2">
<h2 id="org1f42dad"><span class="section-number-2">1</span> Coding conventions</h2>
<div id="outline-container-org13099ac" class="outline-2">
<h2 id="org13099ac"><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-org420d6c1" class="outline-3">
<h3 id="org420d6c1"><span class="section-number-3">1.1</span> Memory allocation</h3>
<div id="outline-container-org34ad392" class="outline-3">
<h3 id="org34ad392"><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-orgcdf88c5" class="outline-2">
<h2 id="orgcdf88c5"><span class="section-number-2">2</span> Front end</h2>
<div id="outline-container-org89e6683" class="outline-2">
<h2 id="org89e6683"><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-orgbd8029a" class="outline-3">
<h3 id="orgbd8029a"><span class="section-number-3">2.1</span> Error handling</h3>
<div id="outline-container-orged21c99" class="outline-3">
<h3 id="orged21c99"><span class="section-number-3">2.1</span> Error handling</h3>
<div class="outline-text-3" id="text-2-1">
<table id="org7d31a40" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgfeb14f4" 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-org6d2dd1c" class="outline-4">
<h4 id="org6d2dd1c"><span class="section-number-4">2.1.1</span> Decoding errors</h4>
<div id="outline-container-org3429912" class="outline-4">
<h4 id="org3429912"><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-orgac101b8" class="outline-5">
<h5 id="orgac101b8"><span class="section-number-5">2.1.1.1</span> C source code</h5>
<div id="outline-container-org30faad5" class="outline-5">
<h5 id="org30faad5"><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-orgf143850" class="outline-5">
<h5 id="orgf143850"><span class="section-number-5">2.1.1.2</span> Fortran interface</h5>
<div id="outline-container-org9f0a40e" class="outline-5">
<h5 id="org9f0a40e"><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-org0138108" class="outline-5">
<h5 id="org0138108"><span class="section-number-5">2.1.1.3</span> Python interface</h5>
<div id="outline-container-org2975392" class="outline-5">
<h5 id="org2975392"><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-orgde370e3" class="outline-3">
<h3 id="orgde370e3"><span class="section-number-3">2.2</span> Back ends</h3>
<div id="outline-container-org7bab42c" class="outline-3">
<h3 id="org7bab42c"><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-org59064d4" class="outline-4">
<h4 id="org59064d4"><span class="section-number-4">2.2.1</span> C</h4>
<div id="outline-container-org95b723d" class="outline-4">
<h4 id="org95b723d"><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-orga6dd3b9" class="outline-4">
<h4 id="orga6dd3b9"><span class="section-number-4">2.2.2</span> Fortran</h4>
<div id="outline-container-org5f9f84d" class="outline-4">
<h4 id="org5f9f84d"><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-orgde9eaac" class="outline-4">
<h4 id="orgde9eaac"><span class="section-number-4">2.2.3</span> Python</h4>
<div id="outline-container-org093eff1" class="outline-4">
<h4 id="org093eff1"><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-org005582c" class="outline-3">
<h3 id="org005582c"><span class="section-number-3">2.3</span> Read/write behavior</h3>
<div id="outline-container-org03ea95b" class="outline-3">
<h3 id="org03ea95b"><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-org54159a7" class="outline-3">
<h3 id="org54159a7"><span class="section-number-3">2.4</span> TREXIO file type</h3>
<div id="outline-container-org9fd6ba6" class="outline-3">
<h3 id="org9fd6ba6"><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-org5c2b930" class="outline-4">
<h4 id="org5c2b930"><span class="section-number-4">2.4.1</span> TREXIO<sub>File</sub> Python class</h4>
<div id="outline-container-org29f9ece" class="outline-4">
<h4 id="org29f9ece"><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-org5f408da" class="outline-3">
<h3 id="org5f408da"><span class="section-number-3">2.5</span> Polymorphism of the file handle</h3>
<div id="outline-container-org2b10759" class="outline-3">
<h3 id="org2b10759"><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-orgf2b055a" class="outline-3">
<h3 id="orgf2b055a"><span class="section-number-3">2.6</span> File opening</h3>
<div id="outline-container-orgd8a709a" class="outline-3">
<h3 id="orgd8a709a"><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-org777a8c9" class="outline-4">
<h4 id="org777a8c9"><span class="section-number-4">2.6.1</span> C</h4>
<div id="outline-container-org7e04aa1" class="outline-4">
<h4 id="org7e04aa1"><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-orga4e2136" class="outline-4">
<h4 id="orga4e2136"><span class="section-number-4">2.6.2</span> Fortran</h4>
<div id="outline-container-org9f61088" class="outline-4">
<h4 id="org9f61088"><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-org17026c9" class="outline-4">
<h4 id="org17026c9"><span class="section-number-4">2.6.3</span> Python</h4>
<div id="outline-container-org4f5d14b" class="outline-4">
<h4 id="org4f5d14b"><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-orgb6f8fa7" class="outline-4">
<h4 id="orgb6f8fa7"><span class="section-number-4">2.6.4</span> Zero-based versus one-based arrays of indices</h4>
<div id="outline-container-org3e354ce" class="outline-4">
<h4 id="org3e354ce"><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-org54fb930" class="outline-3">
<h3 id="org54fb930"><span class="section-number-3">2.7</span> File closing</h3>
<div id="outline-container-orgfc04ec5" class="outline-3">
<h3 id="orgfc04ec5"><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-orgcfd2c85" class="outline-4">
<h4 id="orgcfd2c85"><span class="section-number-4">2.7.1</span> C</h4>
<div id="outline-container-orgdd511cc" class="outline-4">
<h4 id="orgdd511cc"><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-org33208a4" class="outline-4">
<h4 id="org33208a4"><span class="section-number-4">2.7.2</span> Fortran</h4>
<div id="outline-container-org67bd30a" class="outline-4">
<h4 id="org67bd30a"><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-orgeb04f63" class="outline-4">
<h4 id="orgeb04f63"><span class="section-number-4">2.7.3</span> Python</h4>
<div id="outline-container-orgf5fce4c" class="outline-4">
<h4 id="orgf5fce4c"><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-orgb6be22b" class="outline-2">
<h2 id="orgb6be22b"><span class="section-number-2">3</span> Templates for front end</h2>
<div id="outline-container-orgc6de66c" class="outline-2">
<h2 id="orgc6de66c"><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-orgb46c957" class="outline-3">
<h3 id="orgb46c957"><span class="section-number-3">3.1</span> Description</h3>
<div id="outline-container-org5b79f78" class="outline-3">
<h3 id="org5b79f78"><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-org18db8d1" class="outline-3">
<h3 id="org18db8d1"><span class="section-number-3">3.2</span> Templates for front end has/read/write a single numerical attribute</h3>
<div id="outline-container-org16cc9b6" class="outline-3">
<h3 id="org16cc9b6"><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-org93b71c6" class="outline-4">
<h4 id="org93b71c6"><span class="section-number-4">3.2.1</span> Introduction</h4>
<div id="outline-container-orgcdb736c" class="outline-4">
<h4 id="orgcdb736c"><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-orgfa7f415" class="outline-4">
<h4 id="orgfa7f415"><span class="section-number-4">3.2.2</span> C templates for front end</h4>
<div id="outline-container-org1af320d" class="outline-4">
<h4 id="org1af320d"><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-org4e07a06" class="outline-5">
<h5 id="org4e07a06"><span class="section-number-5">3.2.2.1</span> Function declarations</h5>
<div id="outline-container-orgc65667e" class="outline-5">
<h5 id="orgc65667e"><span class="section-number-5">3.2.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-org6539816" class="outline-5">
<h5 id="org6539816"><span class="section-number-5">3.2.2.2</span> Source code for double precision functions</h5>
<div id="outline-container-org35bf507" class="outline-5">
<h5 id="org35bf507"><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-orga8ad191" class="outline-5">
<h5 id="orga8ad191"><span class="section-number-5">3.2.2.3</span> Source code for single precision functions</h5>
<div id="outline-container-org159f0f2" class="outline-5">
<h5 id="org159f0f2"><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-orga47df8b" class="outline-5">
<h5 id="orga47df8b"><span class="section-number-5">3.2.2.4</span> Source code for default functions</h5>
<div id="outline-container-org9c08355" class="outline-5">
<h5 id="org9c08355"><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-orgc1008e0" class="outline-4">
<h4 id="orgc1008e0"><span class="section-number-4">3.2.3</span> Fortran templates for front end</h4>
<div id="outline-container-org6b45a2b" class="outline-4">
<h4 id="org6b45a2b"><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-org734b154" class="outline-4">
<h4 id="org734b154"><span class="section-number-4">3.2.4</span> Python templates for front end</h4>
<div id="outline-container-orga220a91" class="outline-4">
<h4 id="orga220a91"><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-org0607313" class="outline-3">
<h3 id="org0607313"><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-org9e280b5" class="outline-3">
<h3 id="org9e280b5"><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-org24dff52" class="outline-4">
<h4 id="org24dff52"><span class="section-number-4">3.3.1</span> Introduction</h4>
<div id="outline-container-org3e4c230" class="outline-4">
<h4 id="org3e4c230"><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-org233bbeb" class="outline-4">
<h4 id="org233bbeb"><span class="section-number-4">3.3.2</span> C templates for front end</h4>
<div id="outline-container-org884b9d3" class="outline-4">
<h4 id="org884b9d3"><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-org0a85166" class="outline-5">
<h5 id="org0a85166"><span class="section-number-5">3.3.2.1</span> Function declarations</h5>
<div id="outline-container-org0f50274" class="outline-5">
<h5 id="org0f50274"><span class="section-number-5">3.3.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-orgc5b2327" class="outline-5">
<h5 id="orgc5b2327"><span class="section-number-5">3.3.2.2</span> Source code for double precision functions</h5>
<div id="outline-container-org11bf6d1" class="outline-5">
<h5 id="org11bf6d1"><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-orgcd80c5c" class="outline-5">
<h5 id="orgcd80c5c"><span class="section-number-5">3.3.2.3</span> Source code for single precision functions</h5>
<div id="outline-container-orgd305652" class="outline-5">
<h5 id="orgd305652"><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-org316ada3" class="outline-5">
<h5 id="org316ada3"><span class="section-number-5">3.3.2.4</span> Source code for memory-safe functions</h5>
<div id="outline-container-org608a8ed" class="outline-5">
<h5 id="org608a8ed"><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="org4af7168"><span style="color: #228b22;">trexio_exit_code</span> <span style="color: #a0522d;">rc</span>;
<pre class="src src-c" id="org2472dbf"><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-org07ea3b3" class="outline-5">
<h5 id="org07ea3b3"><span class="section-number-5">3.3.2.5</span> Source code for default functions</h5>
<div id="outline-container-orgcbb3bc6" class="outline-5">
<h5 id="orgcbb3bc6"><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-org3222f78" class="outline-4">
<h4 id="org3222f78"><span class="section-number-4">3.3.3</span> Fortran templates for front end</h4>
<div id="outline-container-org0221e05" class="outline-4">
<h4 id="org0221e05"><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-orgb733819" class="outline-4">
<h4 id="orgb733819"><span class="section-number-4">3.3.4</span> Python templates for front end</h4>
<div id="outline-container-org62c9c2a" class="outline-4">
<h4 id="org62c9c2a"><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-org064c06b" class="outline-3">
<h3 id="org064c06b"><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-org9d5d85f" class="outline-3">
<h3 id="org9d5d85f"><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-org1ea1e70" class="outline-4">
<h4 id="org1ea1e70"><span class="section-number-4">3.4.1</span> Introduction</h4>
<div id="outline-container-org571739f" class="outline-4">
<h4 id="org571739f"><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-orge3a9eec" class="outline-4">
<h4 id="orge3a9eec"><span class="section-number-4">3.4.2</span> C templates for front end</h4>
<div id="outline-container-org3df96b6" class="outline-4">
<h4 id="org3df96b6"><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-org518c6f8" class="outline-5">
<h5 id="org518c6f8"><span class="section-number-5">3.4.2.1</span> Function declarations</h5>
<div id="outline-container-orgf089ef4" class="outline-5">
<h5 id="orgf089ef4"><span class="section-number-5">3.4.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-orgd9ecf4a" class="outline-5">
<h5 id="orgd9ecf4a"><span class="section-number-5">3.4.2.2</span> Source code for default functions</h5>
<div id="outline-container-org5311b1f" class="outline-5">
<h5 id="org5311b1f"><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-org45e6cef" class="outline-4">
<h4 id="org45e6cef"><span class="section-number-4">3.4.3</span> Fortran templates for front end</h4>
<div id="outline-container-org7c5f899" class="outline-4">
<h4 id="org7c5f899"><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-orga7e7aa3" class="outline-4">
<h4 id="orga7e7aa3"><span class="section-number-4">3.4.4</span> Python templates for front end</h4>
<div id="outline-container-orgcd49ca5" class="outline-4">
<h4 id="orgcd49ca5"><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-orge55d6c1" class="outline-3">
<h3 id="orge55d6c1"><span class="section-number-3">3.5</span> Templates for front end has/read/write a dataset of strings</h3>
<div id="outline-container-org4f02b0d" class="outline-3">
<h3 id="org4f02b0d"><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-orgb0ad180" class="outline-4">
<h4 id="orgb0ad180"><span class="section-number-4">3.5.1</span> Introduction</h4>
<div id="outline-container-org2901aa7" class="outline-4">
<h4 id="org2901aa7"><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-org98d39aa" class="outline-4">
<h4 id="org98d39aa"><span class="section-number-4">3.5.2</span> C templates for front end</h4>
<div id="outline-container-orge9261ad" class="outline-4">
<h4 id="orge9261ad"><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-org37a0752" class="outline-5">
<h5 id="org37a0752"><span class="section-number-5">3.5.2.1</span> Function declarations</h5>
<div id="outline-container-org3e59e01" class="outline-5">
<h5 id="org3e59e01"><span class="section-number-5">3.5.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-orgdfe738e" class="outline-5">
<h5 id="orgdfe738e"><span class="section-number-5">3.5.2.2</span> Source code for default functions</h5>
<div id="outline-container-orgac2d1a4" class="outline-5">
<h5 id="orgac2d1a4"><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-org3ebd5f9" class="outline-4">
<h4 id="org3ebd5f9"><span class="section-number-4">3.5.3</span> Fortran templates for front end</h4>
<div id="outline-container-orgee973ae" class="outline-4">
<h4 id="orgee973ae"><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-org19b4d9e" class="outline-4">
<h4 id="org19b4d9e"><span class="section-number-4">3.5.4</span> Python templates for front end</h4>
<div id="outline-container-orgfc92d4f" class="outline-4">
<h4 id="orgfc92d4f"><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-org825ed85" class="outline-3">
<h3 id="org825ed85"><span class="section-number-3">3.6</span> Templates for front end has/read/write a single string attribute</h3>
<div id="outline-container-orge1b0164" class="outline-3">
<h3 id="orge1b0164"><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-org970347a" class="outline-4">
<h4 id="org970347a"><span class="section-number-4">3.6.1</span> Introduction</h4>
<div id="outline-container-orgdd4d354" class="outline-4">
<h4 id="orgdd4d354"><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-orgdd5cf69" class="outline-4">
<h4 id="orgdd5cf69"><span class="section-number-4">3.6.2</span> C templates for front end</h4>
<div id="outline-container-org183de38" class="outline-4">
<h4 id="org183de38"><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-org47b3e25" class="outline-5">
<h5 id="org47b3e25"><span class="section-number-5">3.6.2.1</span> Function declarations</h5>
<div id="outline-container-orga50be4c" class="outline-5">
<h5 id="orga50be4c"><span class="section-number-5">3.6.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-org0acd87e" class="outline-5">
<h5 id="org0acd87e"><span class="section-number-5">3.6.2.2</span> Source code for default functions</h5>
<div id="outline-container-org5901247" class="outline-5">
<h5 id="org5901247"><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-org37e265f" class="outline-4">
<h4 id="org37e265f"><span class="section-number-4">3.6.3</span> Fortran templates for front end</h4>
<div id="outline-container-orge63b532" class="outline-4">
<h4 id="orge63b532"><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-orgaf1b596" class="outline-4">
<h4 id="orgaf1b596"><span class="section-number-4">3.6.4</span> Python templates for front end</h4>
<div id="outline-container-org36313bf" class="outline-4">
<h4 id="org36313bf"><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-org24d66f7" class="outline-2">
<h2 id="org24d66f7"><span class="section-number-2">4</span> Fortran helper/wrapper functions</h2>
<div id="outline-container-orgec52913" class="outline-2">
<h2 id="orgec52913"><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: 2022-01-07 Fri 10:59</p>
<p class="date">Created: 2022-01-07 Fri 14:38</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>
<!-- 2022-01-07 Fri 10:59 -->
<!-- 2022-01-07 Fri 14:38 -->
<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="#orgf242665">1. HDF5 back end</a>
<li><a href="#org43d76cd">1. HDF5 back end</a>
<ul>
<li><a href="#orgf3a8f26">1.1. Template for HDF5 definitions</a></li>
<li><a href="#org99c7e01">1.2. Template for HDF5 structures</a></li>
<li><a href="#orgd062364">1.3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgb54ff12">1.4. Template for HDF5 has/read/write the numerical attribute</a></li>
<li><a href="#org3ca7f3f">1.5. Template for HDF5 has/read/write the dataset of numerical data</a></li>
<li><a href="#orgf806735">1.6. Template for HDF5 has/read/write the dataset of sparse data</a></li>
<li><a href="#org417a188">1.7. Template for HDF5 has/read/write the dataset of strings</a></li>
<li><a href="#org8a689b8">1.8. Template for HDF5 has/read/write the string attribute</a></li>
<li><a href="#orge07d0c5">1.9. Helper functions</a></li>
<li><a href="#orgfc8f525">1.1. Template for HDF5 definitions</a></li>
<li><a href="#org2423b82">1.2. Template for HDF5 structures</a></li>
<li><a href="#org7a95c38">1.3. Template for HDF5 init/deinit</a></li>
<li><a href="#org4724dc8">1.4. Template for HDF5 has/read/write the numerical attribute</a></li>
<li><a href="#orgdd821e7">1.5. Template for HDF5 has/read/write the dataset of numerical data</a></li>
<li><a href="#orge383750">1.6. Template for HDF5 has/read/write the dataset of sparse data</a></li>
<li><a href="#orgb1656b6">1.7. Template for HDF5 has/read/write the dataset of strings</a></li>
<li><a href="#orgdac1198">1.8. Template for HDF5 has/read/write the string attribute</a></li>
<li><a href="#org0447ca1">1.9. Helper functions</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-orgf242665" class="outline-2">
<h2 id="orgf242665"><span class="section-number-2">1</span> HDF5 back end</h2>
<div id="outline-container-org43d76cd" class="outline-2">
<h2 id="org43d76cd"><span class="section-number-2">1</span> HDF5 back end</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-orgf3a8f26" class="outline-3">
<h3 id="orgf3a8f26"><span class="section-number-3">1.1</span> Template for HDF5 definitions</h3>
<div id="outline-container-orgfc8f525" class="outline-3">
<h3 id="orgfc8f525"><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-org99c7e01" class="outline-3">
<h3 id="org99c7e01"><span class="section-number-3">1.2</span> Template for HDF5 structures</h3>
<div id="outline-container-org2423b82" class="outline-3">
<h3 id="org2423b82"><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-orgd062364" class="outline-3">
<h3 id="orgd062364"><span class="section-number-3">1.3</span> Template for HDF5 init/deinit</h3>
<div id="outline-container-org7a95c38" class="outline-3">
<h3 id="org7a95c38"><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-orgb54ff12" class="outline-3">
<h3 id="orgb54ff12"><span class="section-number-3">1.4</span> Template for HDF5 has/read/write the numerical attribute</h3>
<div id="outline-container-org4724dc8" class="outline-3">
<h3 id="org4724dc8"><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-org3ca7f3f" class="outline-3">
<h3 id="org3ca7f3f"><span class="section-number-3">1.5</span> Template for HDF5 has/read/write the dataset of numerical data</h3>
<div id="outline-container-orgdd821e7" class="outline-3">
<h3 id="orgdd821e7"><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-orgf806735" class="outline-3">
<h3 id="orgf806735"><span class="section-number-3">1.6</span> Template for HDF5 has/read/write the dataset of sparse data</h3>
<div id="outline-container-orge383750" class="outline-3">
<h3 id="orge383750"><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-org417a188" class="outline-3">
<h3 id="org417a188"><span class="section-number-3">1.7</span> Template for HDF5 has/read/write the dataset of strings</h3>
<div id="outline-container-orgb1656b6" class="outline-3">
<h3 id="orgb1656b6"><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-org8a689b8" class="outline-3">
<h3 id="org8a689b8"><span class="section-number-3">1.8</span> Template for HDF5 has/read/write the string attribute</h3>
<div id="outline-container-orgdac1198" class="outline-3">
<h3 id="orgdac1198"><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-orge07d0c5" class="outline-3">
<h3 id="orge07d0c5"><span class="section-number-3">1.9</span> Helper functions</h3>
<div id="outline-container-org0447ca1" class="outline-3">
<h3 id="org0447ca1"><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: 2022-01-07 Fri 10:59</p>
<p class="date">Created: 2022-01-07 Fri 14:38</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

82
templator_text.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>
<!-- 2022-01-07 Fri 10:59 -->
<!-- 2022-01-07 Fri 14:38 -->
<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="#org287b0ac">1. TEXT back end</a>
<li><a href="#org344602e">1. TEXT back end</a>
<ul>
<li><a href="#orgb24e387">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#orge21f21d">1.2. Template for general structure in text back end</a></li>
<li><a href="#org18324dc">1.3. Initialize function (constant part)</a></li>
<li><a href="#orgde9aab1">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#orgebffde6">1.5. Template for text read struct</a></li>
<li><a href="#org05071a1">1.6. Template for text flush struct</a></li>
<li><a href="#orge20fc67">1.7. Template for text free memory</a></li>
<li><a href="#orgbf54103">1.8. Template for has/read/write the numerical attribute</a></li>
<li><a href="#org4f25518">1.9. Template for has/read/write the dataset of numerical data</a></li>
<li><a href="#org9cec2d8">1.10. Template for has/read/write the dataset of strings</a></li>
<li><a href="#orgfcbe287">1.11. Template for has/read/write the string attribute</a></li>
<li><a href="#org792ab8d">1.12. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org225f7d4">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#org54e5825">1.2. Template for general structure in text back end</a></li>
<li><a href="#org4cf1110">1.3. Initialize function (constant part)</a></li>
<li><a href="#org19b5bc5">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#org592646f">1.5. Template for text read struct</a></li>
<li><a href="#orgc30ffad">1.6. Template for text flush struct</a></li>
<li><a href="#org7040c19">1.7. Template for text free memory</a></li>
<li><a href="#org0d8efd2">1.8. Template for has/read/write the numerical attribute</a></li>
<li><a href="#orgd8514a8">1.9. Template for has/read/write the dataset of numerical data</a></li>
<li><a href="#org28aff21">1.10. Template for has/read/write the dataset of strings</a></li>
<li><a href="#org7e60730">1.11. Template for has/read/write the string attribute</a></li>
<li><a href="#org1b71531">1.12. Template for has/read/write the dataset of sparse data</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org287b0ac" class="outline-2">
<h2 id="org287b0ac"><span class="section-number-2">1</span> TEXT back end</h2>
<div id="outline-container-org344602e" class="outline-2">
<h2 id="org344602e"><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-orgb24e387" class="outline-3">
<h3 id="orgb24e387"><span class="section-number-3">1.1</span> Template for group-related structures in text back end</h3>
<div id="outline-container-org225f7d4" class="outline-3">
<h3 id="org225f7d4"><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-orge21f21d" class="outline-3">
<h3 id="orge21f21d"><span class="section-number-3">1.2</span> Template for general structure in text back end</h3>
<div id="outline-container-org54e5825" class="outline-3">
<h3 id="org54e5825"><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-org18324dc" class="outline-3">
<h3 id="org18324dc"><span class="section-number-3">1.3</span> Initialize function (constant part)</h3>
<div id="outline-container-org4cf1110" class="outline-3">
<h3 id="org4cf1110"><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-orgde9aab1" class="outline-3">
<h3 id="orgde9aab1"><span class="section-number-3">1.4</span> Deinitialize function (templated part)</h3>
<div id="outline-container-org19b5bc5" class="outline-3">
<h3 id="org19b5bc5"><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-orgebffde6" class="outline-3">
<h3 id="orgebffde6"><span class="section-number-3">1.5</span> Template for text read struct</h3>
<div id="outline-container-org592646f" class="outline-3">
<h3 id="org592646f"><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-org05071a1" class="outline-3">
<h3 id="org05071a1"><span class="section-number-3">1.6</span> Template for text flush struct</h3>
<div id="outline-container-orgc30ffad" class="outline-3">
<h3 id="orgc30ffad"><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-orge20fc67" class="outline-3">
<h3 id="orge20fc67"><span class="section-number-3">1.7</span> Template for text free memory</h3>
<div id="outline-container-org7040c19" class="outline-3">
<h3 id="org7040c19"><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-orgbf54103" class="outline-3">
<h3 id="orgbf54103"><span class="section-number-3">1.8</span> Template for has/read/write the numerical attribute</h3>
<div id="outline-container-org0d8efd2" class="outline-3">
<h3 id="org0d8efd2"><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-org4f25518" class="outline-3">
<h3 id="org4f25518"><span class="section-number-3">1.9</span> Template for has/read/write the dataset of numerical data</h3>
<div id="outline-container-orgd8514a8" class="outline-3">
<h3 id="orgd8514a8"><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-org9cec2d8" class="outline-3">
<h3 id="org9cec2d8"><span class="section-number-3">1.10</span> Template for has/read/write the dataset of strings</h3>
<div id="outline-container-org28aff21" class="outline-3">
<h3 id="org28aff21"><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-orgfcbe287" class="outline-3">
<h3 id="orgfcbe287"><span class="section-number-3">1.11</span> Template for has/read/write the string attribute</h3>
<div id="outline-container-org7e60730" class="outline-3">
<h3 id="org7e60730"><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-org792ab8d" class="outline-3">
<h3 id="org792ab8d"><span class="section-number-3">1.12</span> Template for has/read/write the dataset of sparse data</h3>
<div id="outline-container-org1b71531" class="outline-3">
<h3 id="org1b71531"><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: 2022-01-07 Fri 10:59</p>
<p class="date">Created: 2022-01-07 Fri 14:38</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

128
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>
<!-- 2022-01-07 Fri 10:59 -->
<!-- 2022-01-07 Fri 14:38 -->
<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="#orgd278ce2">1. Metadata (metadata group)</a></li>
<li><a href="#org02743e6">2. Electron (electron group)</a></li>
<li><a href="#org87cbfe4">3. Nucleus (nucleus group)</a></li>
<li><a href="#org87d6028">4. Effective core potentials (ecp group)</a>
<li><a href="#orgd33df01">1. Metadata (metadata group)</a></li>
<li><a href="#orgfbf490d">2. Electron (electron group)</a></li>
<li><a href="#org5f13c64">3. Nucleus (nucleus group)</a></li>
<li><a href="#orge579bd6">4. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#orge6db4dc">4.1. Example</a></li>
<li><a href="#org109a974">4.1. Example</a></li>
</ul>
</li>
<li><a href="#org72068da">5. Basis set (basis group)</a>
<li><a href="#org95e999b">5. Basis set (basis group)</a>
<ul>
<li><a href="#org85dc101">5.1. Example</a></li>
<li><a href="#org507bdf9">5.1. Example</a></li>
</ul>
</li>
<li><a href="#orgfdeed0d">6. Atomic orbitals (ao group)</a>
<li><a href="#org547ce36">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="#orgfd1ea84">7. Molecular orbitals (mo group)</a>
<li><a href="#org0e793b4">7. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org17cfba1">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgdcb35b7">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#orgdb062f6">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org92fd6c7">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#org3f2ac8a">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#org9cb4e81">9. Reduced density matrices (rdm group)</a></li>
<li><a href="#org6ce9e41">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#org58380a4">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-orgd278ce2" class="outline-2">
<h2 id="orgd278ce2"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-orgd33df01" class="outline-2">
<h2 id="orgd33df01"><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="orgf90192e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd553f0b" 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-org02743e6" class="outline-2">
<h2 id="org02743e6"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div id="outline-container-orgfbf490d" class="outline-2">
<h2 id="orgfbf490d"><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="org92bf4bd" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org1595be0" 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-org87cbfe4" class="outline-2">
<h2 id="org87cbfe4"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div id="outline-container-org5f13c64" class="outline-2">
<h2 id="org5f13c64"><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="org8b64ec4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc280a82" 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-org87d6028" class="outline-2">
<h2 id="org87d6028"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div id="outline-container-orge579bd6" class="outline-2">
<h2 id="orge579bd6"><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="orged9a1ab" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org11e44fe" 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-orge6db4dc" class="outline-3">
<h3 id="orge6db4dc"><span class="section-number-3">4.1</span> Example</h3>
<div id="outline-container-org109a974" class="outline-3">
<h3 id="org109a974"><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-org72068da" class="outline-2">
<h2 id="org72068da"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div id="outline-container-org95e999b" class="outline-2">
<h2 id="org95e999b"><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="org2440c5f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org660e006" 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-org85dc101" class="outline-3">
<h3 id="org85dc101"><span class="section-number-3">5.1</span> Example</h3>
<div id="outline-container-org507bdf9" class="outline-3">
<h3 id="org507bdf9"><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
@ -1032,18 +1032,17 @@ prim_factor =
</div>
</div>
<div id="outline-container-orgfdeed0d" class="outline-2">
<h2 id="orgfdeed0d"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div id="outline-container-org547ce36" class="outline-2">
<h2 id="org547ce36"><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
construction of all the angular functions of each shell. We
consider two cases for the angular functions: the real-valued
spherical harmonics, and the polynomials in Cartesian coordinates.
In the case of spherical harmonics, the AOs are ordered in
increasing magnetic quantum number (\(-l \le m \le l\)), and in the case
of polynomials we impose the canonical ordering of the
Libint2 library, i.e
In the case of spherical harmonics, the AOs are ordered as
\(0, +1, -1, +2, -2, \dots, +m, -m\) and in the case of polynomials we
impose the canonical (or alphabetical) ordering), i.e
</p>
\begin{eqnarray}
@ -1053,6 +1052,11 @@ f & : & f_{xxx}, f_{xxy}, f_{xxz}, f_{xyy}, f_{xyz}, f_{xzz}, f_{yyy}, f_{yyz},
{\rm etc.} \nonumber
\end{eqnarray}
<p>
Note that there is no exception for \(p\) orbitals in spherical
coordinates: the ordering is \(0,+1,-1\) which corresponds \(p_z, p_x, p_y\).
</p>
<p>
AOs are defined as
</p>
@ -1081,13 +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="#org72068da">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#org95e999b">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="org0bffd8a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgfc200e0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1139,8 +1143,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
</table>
</div>
<div id="outline-container-orgc74c03d" class="outline-3">
<h3 id="ao_one_e"><a id="orgc74c03d"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div id="outline-container-orgc9976da" class="outline-3">
<h3 id="ao_one_e"><a id="orgc9976da"></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}}
@ -1158,7 +1162,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="org1d7335e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org9152867" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1225,8 +1229,8 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-orged0a7a2" class="outline-3">
<h3 id="ao_two_e"><a id="orged0a7a2"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div id="outline-container-orga9f58e0" class="outline-3">
<h3 id="ao_two_e"><a id="orga9f58e0"></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
@ -1247,7 +1251,7 @@ notation.
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
</ul>
<table id="org04c4be4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org181bb60" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1287,10 +1291,10 @@ notation.
</div>
</div>
<div id="outline-container-orgfd1ea84" class="outline-2">
<h2 id="orgfd1ea84"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div id="outline-container-org0e793b4" class="outline-2">
<h2 id="org0e793b4"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div class="outline-text-2" id="text-7">
<table id="org3c6a587" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgfc46bbe" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1356,8 +1360,8 @@ notation.
</table>
</div>
<div id="outline-container-org17cfba1" class="outline-3">
<h3 id="org17cfba1"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div id="outline-container-orgdb062f6" class="outline-3">
<h3 id="orgdb062f6"><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
@ -1365,7 +1369,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org1106156" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org7f8ad3f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1432,8 +1436,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-orgdcb35b7" class="outline-3">
<h3 id="orgdcb35b7"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div id="outline-container-org92fd6c7" class="outline-3">
<h3 id="org92fd6c7"><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
@ -1441,7 +1445,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org4353bbc" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgbdd6b5d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1481,13 +1485,13 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org3f2ac8a" class="outline-2">
<h2 id="org3f2ac8a"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
<div id="outline-container-org6ce9e41" class="outline-2">
<h2 id="org6ce9e41"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
</div>
<div id="outline-container-org9cb4e81" class="outline-2">
<h2 id="org9cb4e81"><span class="section-number-2">9</span> Reduced density matrices (rdm group)</h2>
<div id="outline-container-org58380a4" class="outline-2">
<h2 id="org58380a4"><span class="section-number-2">9</span> Reduced density matrices (rdm group)</h2>
<div class="outline-text-2" id="text-9">
<table id="orga27b399" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org0f519f6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1563,7 +1567,7 @@ the basis of molecular orbitals.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-01-07 Fri 10:59</p>
<p class="date">Created: 2022-01-07 Fri 14:38</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>