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README.html
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<head>
<!-- 2021-12-17 Fri 16:14 -->
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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 />
@ -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: 2021-12-17 Fri 16:14</p>
<p class="date">Created: 2021-12-23 Thu 17:22</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">
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<head>
<!-- 2021-12-17 Fri 16:14 -->
<!-- 2021-12-23 Thu 17:22 -->
<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="#org6ac36fa">1. Accessing sparse quantities</a>
<li><a href="#org798a684">1. Accessing sparse quantities</a>
<ul>
<li><a href="#org76bf5b4">1.1. Fortran</a>
<li><a href="#org961885c">1.1. Fortran</a>
<ul>
<li><a href="#org68ffb54">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org5bd37e3">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org73bf891">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org6a86ab9">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orge116fb6">1.1.5. Allocate memory</a></li>
<li><a href="#org0639c0b">1.1.6. Read one-electron quantities</a></li>
<li><a href="#orgd10fcbf">1.1.7. Read two-electron quantities</a>
<li><a href="#orgb24f836">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org6486017">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgb9dde8e">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org72d2425">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org1df619b">1.1.5. Allocate memory</a></li>
<li><a href="#orgb80e7df">1.1.6. Read one-electron quantities</a></li>
<li><a href="#org5f84e8c">1.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#orgd8374a9">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org82df80a">1.1.7.2. Reduced density matrix</a></li>
<li><a href="#org16fc4d8">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org9baa607">1.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org6d22a63">1.1.8. Compute the energy</a></li>
<li><a href="#org3a5c3f6">1.1.9. Terminate</a></li>
<li><a href="#orgd752ae6">1.1.8. Compute the energy</a></li>
<li><a href="#orgd7175b7">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-org6ac36fa" class="outline-2">
<h2 id="org6ac36fa"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
<div id="outline-container-org798a684" class="outline-2">
<h2 id="org798a684"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-org76bf5b4" class="outline-3">
<h3 id="org76bf5b4"><span class="section-number-3">1.1</span> Fortran</h3>
<div id="outline-container-org961885c" class="outline-3">
<h3 id="org961885c"><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-org68ffb54" class="outline-4">
<h4 id="org68ffb54"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-orgb24f836" class="outline-4">
<h4 id="orgb24f836"><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-org5bd37e3" class="outline-4">
<h4 id="org5bd37e3"><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-org6486017" class="outline-4">
<h4 id="org6486017"><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-org73bf891" class="outline-4">
<h4 id="org73bf891"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orgb9dde8e" class="outline-4">
<h4 id="orgb9dde8e"><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-org6a86ab9" class="outline-4">
<h4 id="org6a86ab9"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org72d2425" class="outline-4">
<h4 id="org72d2425"><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-orge116fb6" class="outline-4">
<h4 id="orge116fb6"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div id="outline-container-org1df619b" class="outline-4">
<h4 id="org1df619b"><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-org0639c0b" class="outline-4">
<h4 id="org0639c0b"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-orgb80e7df" class="outline-4">
<h4 id="orgb80e7df"><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-orgd10fcbf" class="outline-4">
<h4 id="orgd10fcbf"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-org5f84e8c" class="outline-4">
<h4 id="org5f84e8c"><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-orgd8374a9" class="outline-5">
<h5 id="orgd8374a9"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org16fc4d8" class="outline-5">
<h5 id="org16fc4d8"><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-org82df80a" class="outline-5">
<h5 id="org82df80a"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org9baa607" class="outline-5">
<h5 id="org9baa607"><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-org6d22a63" class="outline-4">
<h4 id="org6d22a63"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div id="outline-container-orgd752ae6" class="outline-4">
<h4 id="orgd752ae6"><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-org3a5c3f6" class="outline-4">
<h4 id="org3a5c3f6"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div id="outline-container-orgd7175b7" class="outline-4">
<h4 id="orgd7175b7"><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: 2021-12-17 Fri 16:14</p>
<p class="date">Created: 2021-12-23 Thu 17:22</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>
<!-- 2021-12-17 Fri 16:14 -->
<!-- 2021-12-23 Thu 17:22 -->
<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 />
@ -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: 2021-12-17 Fri 16:14</p>
<p class="date">Created: 2021-12-23 Thu 17:22</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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templator_front.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>
<!-- 2021-12-17 Fri 16:14 -->
<!-- 2021-12-23 Thu 17:22 -->
<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>
@ -333,136 +333,139 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org3b6d891">1. Coding conventions</a>
<li><a href="#org1d3bf8d">1. Coding conventions</a>
<ul>
<li><a href="#orga0b4b82">1.1. Memory allocation</a></li>
<li><a href="#orga3bd889">1.1. Memory allocation</a></li>
</ul>
</li>
<li><a href="#org335fe54">2. Front end</a>
<li><a href="#org9fd529c">2. Front end</a>
<ul>
<li><a href="#orgf4769eb">2.1. Error handling</a>
<li><a href="#org5f34fda">2.1. Error handling</a>
<ul>
<li><a href="#orgefb4139">2.1.1. Decoding errors</a>
<li><a href="#orge95277b">2.1.1. Decoding errors</a>
<ul>
<li><a href="#org303d3ca">2.1.1.1. C source code</a></li>
<li><a href="#orgb7950c5">2.1.1.2. Fortran interface</a></li>
<li><a href="#org840254c">2.1.1.3. Python interface</a></li>
<li><a href="#orga66829a">2.1.1.1. C source code</a></li>
<li><a href="#org5c4de6a">2.1.1.2. Fortran interface</a></li>
<li><a href="#orgb63d12b">2.1.1.3. Python interface</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org37a3a3e">2.2. Back ends</a>
<li><a href="#orgbbb47c9">2.2. Back ends</a>
<ul>
<li><a href="#org6f81ed3">2.2.1. C</a></li>
<li><a href="#org988f74c">2.2.2. Fortran</a></li>
<li><a href="#org845b5b5">2.2.3. Python</a></li>
<li><a href="#orgd0a5290">2.2.1. C</a></li>
<li><a href="#org5644c6b">2.2.2. Fortran</a></li>
<li><a href="#org561c02c">2.2.3. Python</a></li>
</ul>
</li>
<li><a href="#org2fe01e9">2.3. Read/write behavior</a></li>
<li><a href="#orgebb566e">2.4. TREXIO file type</a>
<li><a href="#org81eaa3d">2.3. Read/write behavior</a></li>
<li><a href="#org87a70e6">2.4. TREXIO file type</a>
<ul>
<li><a href="#org04b112a">2.4.1. TREXIO<sub>File</sub> Python class</a></li>
<li><a href="#orgfad6cc6">2.4.1. TREXIO<sub>File</sub> Python class</a></li>
</ul>
</li>
<li><a href="#orga942879">2.5. Polymorphism of the file handle</a></li>
<li><a href="#org0fc0c86">2.6. File opening</a>
<li><a href="#orgd5dcb42">2.5. Polymorphism of the file handle</a></li>
<li><a href="#orgdc48e5e">2.6. File opening</a>
<ul>
<li><a href="#org14396a8">2.6.1. C</a></li>
<li><a href="#org4245c62">2.6.2. Fortran</a></li>
<li><a href="#orge8a04ca">2.6.3. Python</a></li>
<li><a href="#org7d2c5bd">2.6.4. Zero-based versus one-based arrays of indices</a></li>
<li><a href="#org8483dad">2.6.1. C</a></li>
<li><a href="#org4670be7">2.6.2. Fortran</a></li>
<li><a href="#org9421763">2.6.3. Python</a></li>
<li><a href="#org02f8a1c">2.6.4. Zero-based versus one-based arrays of indices</a></li>
</ul>
</li>
<li><a href="#org4623488">2.7. File closing</a>
<li><a href="#orga5f77fd">2.7. File closing</a>
<ul>
<li><a href="#org742637b">2.7.1. C</a></li>
<li><a href="#orgb8ed4c7">2.7.2. Fortran</a></li>
<li><a href="#org0ed7780">2.7.3. Python</a></li>
<li><a href="#org0ab6edc">2.7.1. C</a></li>
<li><a href="#org6cd2146">2.7.2. Fortran</a></li>
<li><a href="#org9073337">2.7.3. Python</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org704d194">3. Templates for front end</a>
<li><a href="#orga419c6a">3. Templates for front end</a>
<ul>
<li><a href="#org0524590">3.1. Description</a></li>
<li><a href="#orga703c8d">3.2. Templates for front end has/read/write a single numerical attribute</a>
<li><a href="#org95aa3f5">3.1. Description</a></li>
<li><a href="#org938646c">3.2. Templates for front end has/read/write a single numerical attribute</a>
<ul>
<li><a href="#org781376b">3.2.1. Introduction</a></li>
<li><a href="#org0f4efb3">3.2.2. C templates for front end</a>
<li><a href="#org4c26200">3.2.1. Introduction</a></li>
<li><a href="#org453871e">3.2.2. C templates for front end</a>
<ul>
<li><a href="#org03fddb5">3.2.2.1. Function declarations</a></li>
<li><a href="#org3d3bdbf">3.2.2.2. Source code for double precision functions</a></li>
<li><a href="#org95a5cbf">3.2.2.3. Source code for single precision functions</a></li>
<li><a href="#org74de2c3">3.2.2.4. Source code for default functions</a></li>
<li><a href="#org9276f11">3.2.2.1. Function declarations</a></li>
<li><a href="#org6face11">3.2.2.2. Source code for double precision functions</a></li>
<li><a href="#org8561960">3.2.2.3. Source code for single precision functions</a></li>
<li><a href="#org1193d2e">3.2.2.4. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#org7818375">3.2.3. Fortran templates for front end</a></li>
<li><a href="#org27529c1">3.2.4. Python templates for front end</a></li>
<li><a href="#org6c983d7">3.2.3. Fortran templates for front end</a></li>
<li><a href="#org11a9d43">3.2.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#orgb82e498">3.3. Templates for front end has/read/write a dataset of numerical data</a>
<li><a href="#org3e22f1c">3.3. Templates for front end has/read/write a dataset of numerical data</a>
<ul>
<li><a href="#org6677d43">3.3.1. Introduction</a></li>
<li><a href="#org6beae1a">3.3.2. C templates for front end</a>
<li><a href="#org91c40e2">3.3.1. Introduction</a></li>
<li><a href="#orgb779071">3.3.2. C templates for front end</a>
<ul>
<li><a href="#orgb8e21e4">3.3.2.1. Function declarations</a></li>
<li><a href="#orgbde0618">3.3.2.2. Source code for double precision functions</a></li>
<li><a href="#orga088216">3.3.2.3. Source code for single precision functions</a></li>
<li><a href="#orge5eb28b">3.3.2.4. Source code for memory-safe functions</a></li>
<li><a href="#orgda894d0">3.3.2.5. Source code for default functions</a></li>
<li><a href="#org413dafb">3.3.2.1. Function declarations</a></li>
<li><a href="#orgac4ea76">3.3.2.2. Source code for double precision functions</a></li>
<li><a href="#org3ec539b">3.3.2.3. Source code for single precision functions</a></li>
<li><a href="#orge05c5c0">3.3.2.4. Source code for memory-safe functions</a></li>
<li><a href="#orgb08f42a">3.3.2.5. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#org399401f">3.3.3. Fortran templates for front end</a></li>
<li><a href="#orgfc37854">3.3.4. Python templates for front end</a></li>
<li><a href="#org27de59f">3.3.3. Fortran templates for front end</a></li>
<li><a href="#org5780265">3.3.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#org883c739">3.4. Templates for front end has/read/write a dataset of sparse data</a>
<li><a href="#org47d5dfb">3.4. Templates for front end has/read/write a dataset of sparse data</a>
<ul>
<li><a href="#orgf765d4a">3.4.1. Introduction</a></li>
<li><a href="#org74e8559">3.4.2. C templates for front end</a>
<li><a href="#orga131aef">3.4.1. Introduction</a></li>
<li><a href="#org2d79c3a">3.4.2. C templates for front end</a>
<ul>
<li><a href="#org28bab11">3.4.2.1. Function declarations</a></li>
<li><a href="#org7a62b98">3.4.2.2. Source code for default functions</a></li>
<li><a href="#orgb3f13d9">3.4.2.1. Function declarations</a></li>
<li><a href="#org745f1ff">3.4.2.2. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#orgeb5511b">3.4.3. Fortran templates for front end</a></li>
<li><a href="#org7b9f10a">3.4.3. Fortran templates for front end</a></li>
</ul>
</li>
<li><a href="#orgaa30b08">3.5. Templates for front end has/read/write a dataset of strings</a>
<li><a href="#org467e884">3.5. Templates for front end has/read/write a dataset of strings</a>
<ul>
<li><a href="#org68ea88c">3.5.1. Introduction</a></li>
<li><a href="#org768faec">3.5.2. C templates for front end</a>
<li><a href="#org3e21611">3.5.1. Introduction</a></li>
<li><a href="#org1d16e4e">3.5.2. C templates for front end</a>
<ul>
<li><a href="#org35e856c">3.5.2.1. Function declarations</a></li>
<li><a href="#org04ac927">3.5.2.2. Source code for default functions</a></li>
<li><a href="#orgccc72ca">3.5.2.1. Function declarations</a></li>
<li><a href="#orge9892ed">3.5.2.2. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#org3bd9808">3.5.3. Fortran templates for front end</a></li>
<li><a href="#org3769bf4">3.5.4. Python templates for front end</a></li>
<li><a href="#orgb15053e">3.5.3. Fortran templates for front end</a></li>
<li><a href="#orge25d8bb">3.5.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#org2c8ca1d">3.6. Templates for front end has/read/write a single string attribute</a>
<li><a href="#org0b008bb">3.6. Templates for front end has/read/write a single string attribute</a>
<ul>
<li><a href="#orga9240c0">3.6.1. Introduction</a></li>
<li><a href="#org7ac24bc">3.6.2. C templates for front end</a>
<li><a href="#org1a0ff6f">3.6.1. Introduction</a></li>
<li><a href="#org735d44c">3.6.2. C templates for front end</a>
<ul>
<li><a href="#org965ff60">3.6.2.1. Function declarations</a></li>
<li><a href="#orgdd008a2">3.6.2.2. Source code for default functions</a></li>
<li><a href="#org66a881d">3.6.2.1. Function declarations</a></li>
<li><a href="#org2a62b63">3.6.2.2. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#orgefa4a40">3.6.3. Fortran templates for front end</a></li>
<li><a href="#orgad9df04">3.6.4. Python templates for front end</a></li>
<li><a href="#orgc462317">3.6.3. Fortran templates for front end</a></li>
<li><a href="#org52a8593">3.6.4. Python templates for front end</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orga0833ce">4. Fortran helper/wrapper functions</a></li>
<li><a href="#org99a73ac">4. Fortran helper/wrapper functions</a></li>
</ul>
</div>
</div>
<p>
B
</p>
<div id="outline-container-org3b6d891" class="outline-2">
<h2 id="org3b6d891"><span class="section-number-2">1</span> Coding conventions</h2>
<div id="outline-container-org1d3bf8d" class="outline-2">
<h2 id="org1d3bf8d"><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>
@ -477,8 +480,8 @@ for the JavaScript code in this tag.
</ul>
</div>
<div id="outline-container-orga0b4b82" class="outline-3">
<h3 id="orga0b4b82"><span class="section-number-3">1.1</span> Memory allocation</h3>
<div id="outline-container-orga3bd889" class="outline-3">
<h3 id="orga3bd889"><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
@ -513,8 +516,8 @@ The maximum string size for the filenames is 4096 characters.
</div>
</div>
<div id="outline-container-org335fe54" class="outline-2">
<h2 id="org335fe54"><span class="section-number-2">2</span> Front end</h2>
<div id="outline-container-org9fd529c" class="outline-2">
<h2 id="org9fd529c"><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.
@ -522,10 +525,10 @@ TREXIO front end is modular, which simplifies implementation of new back ends.
</p>
</div>
<div id="outline-container-orgf4769eb" class="outline-3">
<h3 id="orgf4769eb"><span class="section-number-3">2.1</span> Error handling</h3>
<div id="outline-container-org5f34fda" class="outline-3">
<h3 id="org5f34fda"><span class="section-number-3">2.1</span> Error handling</h3>
<div class="outline-text-3" id="text-2-1">
<table id="org34eeaf4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga0d6085" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -766,8 +769,8 @@ and the corresponding message are not propagated to the source code.
</div>
</div>
<div id="outline-container-orgefb4139" class="outline-4">
<h4 id="orgefb4139"><span class="section-number-4">2.1.1</span> Decoding errors</h4>
<div id="outline-container-orge95277b" class="outline-4">
<h4 id="orge95277b"><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
@ -793,8 +796,8 @@ and the corresponding message are not propagated to the source code.
</p>
</div>
<div id="outline-container-org303d3ca" class="outline-5">
<h5 id="org303d3ca"><span class="section-number-5">2.1.1.1</span> C source code</h5>
<div id="outline-container-orga66829a" class="outline-5">
<h5 id="orga66829a"><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>*
@ -905,8 +908,8 @@ and the corresponding message are not propagated to the source code.
</div>
</div>
<div id="outline-container-orgb7950c5" class="outline-5">
<h5 id="orgb7950c5"><span class="section-number-5">2.1.1.2</span> Fortran interface</h5>
<div id="outline-container-org5c4de6a" class="outline-5">
<h5 id="org5c4de6a"><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>
@ -922,8 +925,8 @@ and the corresponding message are not propagated to the source code.
</div>
</div>
<div id="outline-container-org840254c" class="outline-5">
<h5 id="org840254c"><span class="section-number-5">2.1.1.3</span> Python interface</h5>
<div id="outline-container-orgb63d12b" class="outline-5">
<h5 id="orgb63d12b"><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>):
@ -962,8 +965,8 @@ and the corresponding message are not propagated to the source code.
</div>
</div>
<div id="outline-container-org37a3a3e" class="outline-3">
<h3 id="org37a3a3e"><span class="section-number-3">2.2</span> Back ends</h3>
<div id="outline-container-orgbbb47c9" class="outline-3">
<h3 id="orgbbb47c9"><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:
@ -987,8 +990,8 @@ lines that correspond to the <code>TREXIO_JSON</code> back end (not implemented
</p>
</div>
<div id="outline-container-org6f81ed3" class="outline-4">
<h4 id="org6f81ed3"><span class="section-number-4">2.2.1</span> C</h4>
<div id="outline-container-orgd0a5290" class="outline-4">
<h4 id="orgd0a5290"><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>;
@ -1031,8 +1034,8 @@ This is useful due to the fact that HDF5 back end can be disabled at configure s
</div>
</div>
<div id="outline-container-org988f74c" class="outline-4">
<h4 id="org988f74c"><span class="section-number-4">2.2.2</span> Fortran</h4>
<div id="outline-container-org5644c6b" class="outline-4">
<h4 id="org5644c6b"><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>
@ -1058,8 +1061,8 @@ The function below is a Fortran interface for the aforementioned C-compatible <c
</div>
</div>
<div id="outline-container-org845b5b5" class="outline-4">
<h4 id="org845b5b5"><span class="section-number-4">2.2.3</span> Python</h4>
<div id="outline-container-org561c02c" class="outline-4">
<h4 id="org561c02c"><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>
@ -1073,8 +1076,8 @@ The function below is a Fortran interface for the aforementioned C-compatible <c
</div>
</div>
<div id="outline-container-org2fe01e9" class="outline-3">
<h3 id="org2fe01e9"><span class="section-number-3">2.3</span> Read/write behavior</h3>
<div id="outline-container-org81eaa3d" class="outline-3">
<h3 id="org81eaa3d"><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
@ -1102,8 +1105,8 @@ concurrent programs, the behavior is not specified.
</p>
</div>
</div>
<div id="outline-container-orgebb566e" class="outline-3">
<h3 id="orgebb566e"><span class="section-number-3">2.4</span> TREXIO file type</h3>
<div id="outline-container-org87a70e6" class="outline-3">
<h3 id="org87a70e6"><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
@ -1137,8 +1140,8 @@ TREXIO files will have as a first argument the TREXIO file handle.
</div>
</div>
<div id="outline-container-org04b112a" class="outline-4">
<h4 id="org04b112a"><span class="section-number-4">2.4.1</span> TREXIO<sub>File</sub> Python class</h4>
<div id="outline-container-orgfad6cc6" class="outline-4">
<h4 id="orgfad6cc6"><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>:
@ -1211,8 +1214,8 @@ TREXIO files will have as a first argument the TREXIO file handle.
</div>
</div>
<div id="outline-container-orga942879" class="outline-3">
<h3 id="orga942879"><span class="section-number-3">2.5</span> Polymorphism of the file handle</h3>
<div id="outline-container-orgd5dcb42" class="outline-3">
<h3 id="orgd5dcb42"><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
@ -1231,8 +1234,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org0fc0c86" class="outline-3">
<h3 id="org0fc0c86"><span class="section-number-3">2.6</span> File opening</h3>
<div id="outline-container-orgdc48e5e" class="outline-3">
<h3 id="orgdc48e5e"><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.
@ -1271,8 +1274,8 @@ renaming the <code>.txt</code> data files.
</p>
</div>
<div id="outline-container-org14396a8" class="outline-4">
<h4 id="org14396a8"><span class="section-number-4">2.6.1</span> C</h4>
<div id="outline-container-org8483dad" class="outline-4">
<h4 id="org8483dad"><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>*
@ -1458,8 +1461,8 @@ renaming the <code>.txt</code> data files.
</div>
</div>
<div id="outline-container-org4245c62" class="outline-4">
<h4 id="org4245c62"><span class="section-number-4">2.6.2</span> Fortran</h4>
<div id="outline-container-org4670be7" class="outline-4">
<h4 id="org4670be7"><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>
@ -1477,8 +1480,8 @@ renaming the <code>.txt</code> data files.
</div>
</div>
<div id="outline-container-orge8a04ca" class="outline-4">
<h4 id="orge8a04ca"><span class="section-number-4">2.6.3</span> Python</h4>
<div id="outline-container-org9421763" class="outline-4">
<h4 id="org9421763"><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>):
@ -1526,8 +1529,8 @@ renaming the <code>.txt</code> data files.
</div>
</div>
<div id="outline-container-org7d2c5bd" class="outline-4">
<h4 id="org7d2c5bd"><span class="section-number-4">2.6.4</span> Zero-based versus one-based arrays of indices</h4>
<div id="outline-container-org02f8a1c" class="outline-4">
<h4 id="org02f8a1c"><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
@ -1560,8 +1563,8 @@ know if we need to shift by 1 arrays of indices.
</div>
</div>
<div id="outline-container-org4623488" class="outline-3">
<h3 id="org4623488"><span class="section-number-3">2.7</span> File closing</h3>
<div id="outline-container-orga5f77fd" class="outline-3">
<h3 id="orga5f77fd"><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.
@ -1578,8 +1581,8 @@ output:
</p>
</div>
<div id="outline-container-org742637b" class="outline-4">
<h4 id="org742637b"><span class="section-number-4">2.7.1</span> C</h4>
<div id="outline-container-org0ab6edc" class="outline-4">
<h4 id="org0ab6edc"><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>
@ -1658,8 +1661,8 @@ output:
</div>
</div>
<div id="outline-container-orgb8ed4c7" class="outline-4">
<h4 id="orgb8ed4c7"><span class="section-number-4">2.7.2</span> Fortran</h4>
<div id="outline-container-org6cd2146" class="outline-4">
<h4 id="org6cd2146"><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>
@ -1673,8 +1676,8 @@ output:
</div>
</div>
<div id="outline-container-org0ed7780" class="outline-4">
<h4 id="org0ed7780"><span class="section-number-4">2.7.3</span> Python</h4>
<div id="outline-container-org9073337" class="outline-4">
<h4 id="org9073337"><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):
@ -1696,12 +1699,12 @@ output:
</div>
</div>
<div id="outline-container-org704d194" class="outline-2">
<h2 id="org704d194"><span class="section-number-2">3</span> Templates for front end</h2>
<div id="outline-container-orga419c6a" class="outline-2">
<h2 id="orga419c6a"><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-org0524590" class="outline-3">
<h3 id="org0524590"><span class="section-number-3">3.1</span> Description</h3>
<div id="outline-container-org95aa3f5" class="outline-3">
<h3 id="org95aa3f5"><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>:
@ -1922,12 +1925,12 @@ value will result in <code>TREXIO_INVALID_ARG_2</code> exit code.
</div>
</div>
<div id="outline-container-orga703c8d" class="outline-3">
<h3 id="orga703c8d"><span class="section-number-3">3.2</span> Templates for front end has/read/write a single numerical attribute</h3>
<div id="outline-container-org938646c" class="outline-3">
<h3 id="org938646c"><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-org781376b" class="outline-4">
<h4 id="org781376b"><span class="section-number-4">3.2.1</span> Introduction</h4>
<div id="outline-container-org4c26200" class="outline-4">
<h4 id="org4c26200"><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,
@ -1998,8 +2001,8 @@ namely single value of int/float types.
</div>
</div>
<div id="outline-container-org0f4efb3" class="outline-4">
<h4 id="org0f4efb3"><span class="section-number-4">3.2.2</span> C templates for front end</h4>
<div id="outline-container-org453871e" class="outline-4">
<h4 id="org453871e"><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
@ -2013,12 +2016,12 @@ precision (see Table above).
</p>
</div>
<div id="outline-container-org03fddb5" class="outline-5">
<h5 id="org03fddb5"><span class="section-number-5">3.2.2.1</span> Function declarations</h5>
<div id="outline-container-org9276f11" class="outline-5">
<h5 id="org9276f11"><span class="section-number-5">3.2.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-org3d3bdbf" class="outline-5">
<h5 id="org3d3bdbf"><span class="section-number-5">3.2.2.2</span> Source code for double precision functions</h5>
<div id="outline-container-org6face11" class="outline-5">
<h5 id="org6face11"><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>
@ -2087,8 +2090,8 @@ precision (see Table above).
</div>
</div>
<div id="outline-container-org95a5cbf" class="outline-5">
<h5 id="org95a5cbf"><span class="section-number-5">3.2.2.3</span> Source code for single precision functions</h5>
<div id="outline-container-org8561960" class="outline-5">
<h5 id="org8561960"><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 +2167,8 @@ precision (see Table above).
</div>
</div>
<div id="outline-container-org74de2c3" class="outline-5">
<h5 id="org74de2c3"><span class="section-number-5">3.2.2.4</span> Source code for default functions</h5>
<div id="outline-container-org1193d2e" class="outline-5">
<h5 id="org1193d2e"><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>
@ -2222,8 +2225,8 @@ precision (see Table above).
</div>
</div>
<div id="outline-container-org7818375" class="outline-4">
<h4 id="org7818375"><span class="section-number-4">3.2.3</span> Fortran templates for front end</h4>
<div id="outline-container-org6c983d7" class="outline-4">
<h4 id="org6c983d7"><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.
@ -2308,8 +2311,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-org27529c1" class="outline-4">
<h4 id="org27529c1"><span class="section-number-4">3.2.4</span> Python templates for front end</h4>
<div id="outline-container-org11a9d43" class="outline-4">
<h4 id="org11a9d43"><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>:
@ -2394,12 +2397,12 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-orgb82e498" class="outline-3">
<h3 id="orgb82e498"><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-org3e22f1c" class="outline-3">
<h3 id="org3e22f1c"><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-org6677d43" class="outline-4">
<h4 id="org6677d43"><span class="section-number-4">3.3.1</span> Introduction</h4>
<div id="outline-container-org91c40e2" class="outline-4">
<h4 id="org91c40e2"><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.
@ -2481,8 +2484,8 @@ This section concerns API calls related to datasets.
</div>
</div>
<div id="outline-container-org6beae1a" class="outline-4">
<h4 id="org6beae1a"><span class="section-number-4">3.3.2</span> C templates for front end</h4>
<div id="outline-container-orgb779071" class="outline-4">
<h4 id="orgb779071"><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.
@ -2493,12 +2496,12 @@ The basic (non-suffixed) API call on datasets deals with double precision (see T
</p>
</div>
<div id="outline-container-orgb8e21e4" class="outline-5">
<h5 id="orgb8e21e4"><span class="section-number-5">3.3.2.1</span> Function declarations</h5>
<div id="outline-container-org413dafb" class="outline-5">
<h5 id="org413dafb"><span class="section-number-5">3.3.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-orgbde0618" class="outline-5">
<h5 id="orgbde0618"><span class="section-number-5">3.3.2.2</span> Source code for double precision functions</h5>
<div id="outline-container-orgac4ea76" class="outline-5">
<h5 id="orgac4ea76"><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>
@ -2634,8 +2637,8 @@ The basic (non-suffixed) API call on datasets deals with double precision (see T
</div>
</div>
<div id="outline-container-orga088216" class="outline-5">
<h5 id="orga088216"><span class="section-number-5">3.3.2.3</span> Source code for single precision functions</h5>
<div id="outline-container-org3ec539b" class="outline-5">
<h5 id="org3ec539b"><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>
@ -2784,11 +2787,11 @@ The basic (non-suffixed) API call on datasets deals with double precision (see T
</div>
</div>
<div id="outline-container-orge5eb28b" class="outline-5">
<h5 id="orge5eb28b"><span class="section-number-5">3.3.2.4</span> Source code for memory-safe functions</h5>
<div id="outline-container-orge05c5c0" class="outline-5">
<h5 id="orge05c5c0"><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="org0f82b62"><span style="color: #228b22;">trexio_exit_code</span> <span style="color: #a0522d;">rc</span>;
<pre class="src src-c" id="orgf5cd8df"><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>*/
@ -2944,8 +2947,8 @@ rc = trexio_read_$group_dset_dim$_64(file, &amp;($group_dset_dim$));
</div>
</div>
<div id="outline-container-orgda894d0" class="outline-5">
<h5 id="orgda894d0"><span class="section-number-5">3.3.2.5</span> Source code for default functions</h5>
<div id="outline-container-orgb08f42a" class="outline-5">
<h5 id="orgb08f42a"><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>
@ -3023,8 +3026,8 @@ rc = trexio_read_$group_dset_dim$_64(file, &amp;($group_dset_dim$));
</div>
</div>
<div id="outline-container-org399401f" class="outline-4">
<h4 id="org399401f"><span class="section-number-4">3.3.3</span> Fortran templates for front end</h4>
<div id="outline-container-org27de59f" class="outline-4">
<h4 id="org27de59f"><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>.
@ -3109,8 +3112,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-orgfc37854" class="outline-4">
<h4 id="orgfc37854"><span class="section-number-4">3.3.4</span> Python templates for front end</h4>
<div id="outline-container-org5780265" class="outline-4">
<h4 id="org5780265"><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>:
@ -3305,12 +3308,12 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-org883c739" class="outline-3">
<h3 id="org883c739"><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-org47d5dfb" class="outline-3">
<h3 id="org47d5dfb"><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-orgf765d4a" class="outline-4">
<h4 id="orgf765d4a"><span class="section-number-4">3.4.1</span> Introduction</h4>
<div id="outline-container-orga131aef" class="outline-4">
<h4 id="orga131aef"><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
@ -3373,16 +3376,16 @@ the values of the integrals, or only the indices.
</div>
</div>
<div id="outline-container-org74e8559" class="outline-4">
<h4 id="org74e8559"><span class="section-number-4">3.4.2</span> C templates for front end</h4>
<div id="outline-container-org2d79c3a" class="outline-4">
<h4 id="org2d79c3a"><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-org28bab11" class="outline-5">
<h5 id="org28bab11"><span class="section-number-5">3.4.2.1</span> Function declarations</h5>
<div id="outline-container-orgb3f13d9" class="outline-5">
<h5 id="orgb3f13d9"><span class="section-number-5">3.4.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-org7a62b98" class="outline-5">
<h5 id="org7a62b98"><span class="section-number-5">3.4.2.2</span> Source code for default functions</h5>
<div id="outline-container-org745f1ff" class="outline-5">
<h5 id="org745f1ff"><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>
@ -3601,8 +3604,8 @@ the values of the integrals, or only the indices.
</div>
</div>
<div id="outline-container-orgeb5511b" class="outline-4">
<h4 id="orgeb5511b"><span class="section-number-4">3.4.3</span> Fortran templates for front end</h4>
<div id="outline-container-org7b9f10a" class="outline-4">
<h4 id="org7b9f10a"><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>.
@ -3666,12 +3669,12 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-orgaa30b08" class="outline-3">
<h3 id="orgaa30b08"><span class="section-number-3">3.5</span> Templates for front end has/read/write a dataset of strings</h3>
<div id="outline-container-org467e884" class="outline-3">
<h3 id="org467e884"><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-org68ea88c" class="outline-4">
<h4 id="org68ea88c"><span class="section-number-4">3.5.1</span> Introduction</h4>
<div id="outline-container-org3e21611" class="outline-4">
<h4 id="org3e21611"><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.
@ -3711,8 +3714,8 @@ This section concerns API calls related to datasets of strings.
</div>
</div>
<div id="outline-container-org768faec" class="outline-4">
<h4 id="org768faec"><span class="section-number-4">3.5.2</span> C templates for front end</h4>
<div id="outline-container-org1d16e4e" class="outline-4">
<h4 id="org1d16e4e"><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
@ -3720,12 +3723,12 @@ to/from the <code>TREXIO</code> file (except for <code>trexio_has_</code> functi
</p>
</div>
<div id="outline-container-org35e856c" class="outline-5">
<h5 id="org35e856c"><span class="section-number-5">3.5.2.1</span> Function declarations</h5>
<div id="outline-container-orgccc72ca" class="outline-5">
<h5 id="orgccc72ca"><span class="section-number-5">3.5.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-org04ac927" class="outline-5">
<h5 id="org04ac927"><span class="section-number-5">3.5.2.2</span> Source code for default functions</h5>
<div id="outline-container-orge9892ed" class="outline-5">
<h5 id="orge9892ed"><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>
@ -3979,8 +3982,8 @@ to/from the <code>TREXIO</code> file (except for <code>trexio_has_</code> functi
</div>
</div>
<div id="outline-container-org3bd9808" class="outline-4">
<h4 id="org3bd9808"><span class="section-number-4">3.5.3</span> Fortran templates for front end</h4>
<div id="outline-container-orgb15053e" class="outline-4">
<h4 id="orgb15053e"><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>.
@ -4076,8 +4079,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-org3769bf4" class="outline-4">
<h4 id="org3769bf4"><span class="section-number-4">3.5.4</span> Python templates for front end</h4>
<div id="outline-container-orge25d8bb" class="outline-4">
<h4 id="orge25d8bb"><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>:
@ -4193,12 +4196,12 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-org2c8ca1d" class="outline-3">
<h3 id="org2c8ca1d"><span class="section-number-3">3.6</span> Templates for front end has/read/write a single string attribute</h3>
<div id="outline-container-org0b008bb" class="outline-3">
<h3 id="org0b008bb"><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-orga9240c0" class="outline-4">
<h4 id="orga9240c0"><span class="section-number-4">3.6.1</span> Introduction</h4>
<div id="outline-container-org1a0ff6f" class="outline-4">
<h4 id="org1a0ff6f"><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.
@ -4238,16 +4241,16 @@ This section concerns API calls related to string attributes.
</div>
</div>
<div id="outline-container-org7ac24bc" class="outline-4">
<h4 id="org7ac24bc"><span class="section-number-4">3.6.2</span> C templates for front end</h4>
<div id="outline-container-org735d44c" class="outline-4">
<h4 id="org735d44c"><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-org965ff60" class="outline-5">
<h5 id="org965ff60"><span class="section-number-5">3.6.2.1</span> Function declarations</h5>
<div id="outline-container-org66a881d" class="outline-5">
<h5 id="org66a881d"><span class="section-number-5">3.6.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-orgdd008a2" class="outline-5">
<h5 id="orgdd008a2"><span class="section-number-5">3.6.2.2</span> Source code for default functions</h5>
<div id="outline-container-org2a62b63" class="outline-5">
<h5 id="org2a62b63"><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>
@ -4359,8 +4362,8 @@ This section concerns API calls related to string attributes.
</div>
</div>
<div id="outline-container-orgefa4a40" class="outline-4">
<h4 id="orgefa4a40"><span class="section-number-4">3.6.3</span> Fortran templates for front end</h4>
<div id="outline-container-orgc462317" class="outline-4">
<h4 id="orgc462317"><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.
@ -4437,8 +4440,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-orgad9df04" class="outline-4">
<h4 id="orgad9df04"><span class="section-number-4">3.6.4</span> Python templates for front end</h4>
<div id="outline-container-org52a8593" class="outline-4">
<h4 id="org52a8593"><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>:
@ -4528,8 +4531,8 @@ These templates are based on the use of <code>iso_c_binding</code>. Pointers hav
</div>
</div>
<div id="outline-container-orga0833ce" class="outline-2">
<h2 id="orga0833ce"><span class="section-number-2">4</span> Fortran helper/wrapper functions</h2>
<div id="outline-container-org99a73ac" class="outline-2">
<h2 id="org99a73ac"><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.
@ -4664,7 +4667,7 @@ two code are identical, i.e. if the <code>assert</code> statement pass.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2021-12-17 Fri 16:14</p>
<p class="date">Created: 2021-12-23 Thu 17:22</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

64
templator_hdf5.html
View File

@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2021-12-17 Fri 16:14 -->
<!-- 2021-12-23 Thu 17:22 -->
<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="#org49b8ff8">1. HDF5 back end</a>
<li><a href="#org5e2cb01">1. HDF5 back end</a>
<ul>
<li><a href="#org486e7be">1.1. Template for HDF5 definitions</a></li>
<li><a href="#org7936c21">1.2. Template for HDF5 structures</a></li>
<li><a href="#org0b58f3e">1.3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgd21a866">1.4. Template for HDF5 has/read/write the numerical attribute</a></li>
<li><a href="#org454fa3a">1.5. Template for HDF5 has/read/write the dataset of numerical data</a></li>
<li><a href="#org3c302ca">1.6. Template for HDF5 has/read/write the dataset of sparse data</a></li>
<li><a href="#orgf84001c">1.7. Template for HDF5 has/read/write the dataset of strings</a></li>
<li><a href="#orge2b8732">1.8. Template for HDF5 has/read/write the string attribute</a></li>
<li><a href="#orga0ed807">1.9. Helper functions</a></li>
<li><a href="#org5582ec9">1.1. Template for HDF5 definitions</a></li>
<li><a href="#org4b8ebe7">1.2. Template for HDF5 structures</a></li>
<li><a href="#org20a6845">1.3. Template for HDF5 init/deinit</a></li>
<li><a href="#org99d224a">1.4. Template for HDF5 has/read/write the numerical attribute</a></li>
<li><a href="#org66b2b1a">1.5. Template for HDF5 has/read/write the dataset of numerical data</a></li>
<li><a href="#orgfd64d4a">1.6. Template for HDF5 has/read/write the dataset of sparse data</a></li>
<li><a href="#org28cf174">1.7. Template for HDF5 has/read/write the dataset of strings</a></li>
<li><a href="#org2272c5f">1.8. Template for HDF5 has/read/write the string attribute</a></li>
<li><a href="#orgc343fc8">1.9. Helper functions</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org49b8ff8" class="outline-2">
<h2 id="org49b8ff8"><span class="section-number-2">1</span> HDF5 back end</h2>
<div id="outline-container-org5e2cb01" class="outline-2">
<h2 id="org5e2cb01"><span class="section-number-2">1</span> HDF5 back end</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-org486e7be" class="outline-3">
<h3 id="org486e7be"><span class="section-number-3">1.1</span> Template for HDF5 definitions</h3>
<div id="outline-container-org5582ec9" class="outline-3">
<h3 id="org5582ec9"><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-org7936c21" class="outline-3">
<h3 id="org7936c21"><span class="section-number-3">1.2</span> Template for HDF5 structures</h3>
<div id="outline-container-org4b8ebe7" class="outline-3">
<h3 id="org4b8ebe7"><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-org0b58f3e" class="outline-3">
<h3 id="org0b58f3e"><span class="section-number-3">1.3</span> Template for HDF5 init/deinit</h3>
<div id="outline-container-org20a6845" class="outline-3">
<h3 id="org20a6845"><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-orgd21a866" class="outline-3">
<h3 id="orgd21a866"><span class="section-number-3">1.4</span> Template for HDF5 has/read/write the numerical attribute</h3>
<div id="outline-container-org99d224a" class="outline-3">
<h3 id="org99d224a"><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-org454fa3a" class="outline-3">
<h3 id="org454fa3a"><span class="section-number-3">1.5</span> Template for HDF5 has/read/write the dataset of numerical data</h3>
<div id="outline-container-org66b2b1a" class="outline-3">
<h3 id="org66b2b1a"><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>
@ -660,8 +660,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org3c302ca" class="outline-3">
<h3 id="org3c302ca"><span class="section-number-3">1.6</span> Template for HDF5 has/read/write the dataset of sparse data</h3>
<div id="outline-container-orgfd64d4a" class="outline-3">
<h3 id="orgfd64d4a"><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
@ -862,8 +862,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-orgf84001c" class="outline-3">
<h3 id="orgf84001c"><span class="section-number-3">1.7</span> Template for HDF5 has/read/write the dataset of strings</h3>
<div id="outline-container-org28cf174" class="outline-3">
<h3 id="org28cf174"><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>
@ -1068,8 +1068,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-orge2b8732" class="outline-3">
<h3 id="orge2b8732"><span class="section-number-3">1.8</span> Template for HDF5 has/read/write the string attribute</h3>
<div id="outline-container-org2272c5f" class="outline-3">
<h3 id="org2272c5f"><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>
@ -1192,8 +1192,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
</div>
<div id="outline-container-orga0ed807" class="outline-3">
<h3 id="orga0ed807"><span class="section-number-3">1.9</span> Helper functions</h3>
<div id="outline-container-orgc343fc8" class="outline-3">
<h3 id="orgc343fc8"><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>
@ -1443,7 +1443,7 @@ 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: 2021-12-17 Fri 16:14</p>
<p class="date">Created: 2021-12-23 Thu 17:22</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

97
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>
<!-- 2021-12-17 Fri 16:14 -->
<!-- 2021-12-23 Thu 17:22 -->
<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="#orgb6137fc">1. TEXT back end</a>
<li><a href="#org0a03465">1. TEXT back end</a>
<ul>
<li><a href="#org3b6d6e0">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#orgca531b9">1.2. Template for general structure in text back end</a></li>
<li><a href="#orgb9e5edc">1.3. Initialize function (constant part)</a></li>
<li><a href="#org85aea02">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#orgcc6ff55">1.5. Template for text read struct</a></li>
<li><a href="#orge4ef072">1.6. Template for text flush struct</a></li>
<li><a href="#org50aeb6d">1.7. Template for text free memory</a></li>
<li><a href="#orgd9d26b4">1.8. Template for has/read/write the numerical attribute</a></li>
<li><a href="#orgd38d1f4">1.9. Template for has/read/write the dataset of numerical data</a></li>
<li><a href="#org4ee4f98">1.10. Template for has/read/write the dataset of strings</a></li>
<li><a href="#orge83df4c">1.11. Template for has/read/write the string attribute</a></li>
<li><a href="#org71ffd4f">1.12. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org10d1ab6">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#org6ce7c97">1.2. Template for general structure in text back end</a></li>
<li><a href="#org1bb1bf4">1.3. Initialize function (constant part)</a></li>
<li><a href="#org5194ff4">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#org0b927c9">1.5. Template for text read struct</a></li>
<li><a href="#orgbf44b52">1.6. Template for text flush struct</a></li>
<li><a href="#orgbb390e1">1.7. Template for text free memory</a></li>
<li><a href="#org9e1b308">1.8. Template for has/read/write the numerical attribute</a></li>
<li><a href="#orgaddba62">1.9. Template for has/read/write the dataset of numerical data</a></li>
<li><a href="#org2a2ef3e">1.10. Template for has/read/write the dataset of strings</a></li>
<li><a href="#orgfca58bb">1.11. Template for has/read/write the string attribute</a></li>
<li><a href="#org2ca6733">1.12. Template for has/read/write the dataset of sparse data</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-orgb6137fc" class="outline-2">
<h2 id="orgb6137fc"><span class="section-number-2">1</span> TEXT back end</h2>
<div id="outline-container-org0a03465" class="outline-2">
<h2 id="org0a03465"><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-org3b6d6e0" class="outline-3">
<h3 id="org3b6d6e0"><span class="section-number-3">1.1</span> Template for group-related structures in text back end</h3>
<div id="outline-container-org10d1ab6" class="outline-3">
<h3 id="org10d1ab6"><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-orgca531b9" class="outline-3">
<h3 id="orgca531b9"><span class="section-number-3">1.2</span> Template for general structure in text back end</h3>
<div id="outline-container-org6ce7c97" class="outline-3">
<h3 id="org6ce7c97"><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-orgb9e5edc" class="outline-3">
<h3 id="orgb9e5edc"><span class="section-number-3">1.3</span> Initialize function (constant part)</h3>
<div id="outline-container-org1bb1bf4" class="outline-3">
<h3 id="org1bb1bf4"><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-org85aea02" class="outline-3">
<h3 id="org85aea02"><span class="section-number-3">1.4</span> Deinitialize function (templated part)</h3>
<div id="outline-container-org5194ff4" class="outline-3">
<h3 id="org5194ff4"><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-orgcc6ff55" class="outline-3">
<h3 id="orgcc6ff55"><span class="section-number-3">1.5</span> Template for text read struct</h3>
<div id="outline-container-org0b927c9" class="outline-3">
<h3 id="org0b927c9"><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*
@ -774,10 +774,12 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
// <span style="color: #b22222;">END REPEAT GROUP_DSET_NUM</span>
// <span style="color: #b22222;">START REPEAT GROUP_DSET_STR</span>
rc = fscanf(f, <span style="color: #8b2252;">"%1023s"</span>, buffer);
assert(!((rc != 1) || (strcmp(buffer, <span style="color: #8b2252;">"$group_dset$"</span>) != 0)));
/* <span style="color: #b22222;">Allocate arrays </span>*/
<span style="color: #a020f0;">if</span>(size_$group_dset$ != 0) {
$group$-&gt;$group_dset$ = CALLOC(size_$group_dset$, $group_dset_dtype$);
assert (!($group$-&gt;$group_dset$ == <span style="color: #008b8b;">NULL</span>));
<span style="color: #a020f0;">if</span> ($group$-&gt;$group_dset$ == <span style="color: #008b8b;">NULL</span>) {
FREE(buffer);
fclose(f);
@ -786,16 +788,6 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
<span style="color: #a020f0;">return</span> <span style="color: #008b8b;">NULL</span>;
}
rc = fscanf(f, <span style="color: #8b2252;">"%1023s"</span>, buffer);
assert(!((rc != 1) || (strcmp(buffer, <span style="color: #8b2252;">"$group_dset$"</span>) != 0)));
<span style="color: #a020f0;">if</span> ((rc != 1) || (strcmp(buffer, <span style="color: #8b2252;">"$group_dset$"</span>) != 0)) {
FREE(buffer);
fclose(f);
FREE($group$-&gt;$group_dset$);
FREE($group$);
<span style="color: #a020f0;">return</span> <span style="color: #008b8b;">NULL</span>;
}
/* <span style="color: #b22222;">WARNING: this tmp array allows to avoid allocation of space for each element of array of string</span>
<span style="color: #b22222;"> BUT it's size has to be number_of_str*max_len_str where max_len_str is somewhat arbitrary, e.g. 32.</span>
<span style="color: #b22222;"> </span>*/
@ -813,6 +805,7 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
FREE(buffer);
fclose(f);
FREE($group$-&gt;$group_dset$);
FREE(tmp_$group_dset$);
FREE($group$);
<span style="color: #a020f0;">return</span> <span style="color: #008b8b;">NULL</span>;
}
@ -837,8 +830,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-orge4ef072" class="outline-3">
<h3 id="orge4ef072"><span class="section-number-3">1.6</span> Template for text flush struct</h3>
<div id="outline-container-orgbf44b52" class="outline-3">
<h3 id="orgbf44b52"><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>
@ -903,8 +896,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org50aeb6d" class="outline-3">
<h3 id="org50aeb6d"><span class="section-number-3">1.7</span> Template for text free memory</h3>
<div id="outline-container-orgbb390e1" class="outline-3">
<h3 id="orgbb390e1"><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.
@ -949,8 +942,8 @@ Memory is allocated when reading. The following function frees memory.
</div>
</div>
<div id="outline-container-orgd9d26b4" class="outline-3">
<h3 id="orgd9d26b4"><span class="section-number-3">1.8</span> Template for has/read/write the numerical attribute</h3>
<div id="outline-container-org9e1b308" class="outline-3">
<h3 id="org9e1b308"><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>
@ -1013,8 +1006,8 @@ Memory is allocated when reading. The following function frees memory.
</div>
</div>
<div id="outline-container-orgd38d1f4" class="outline-3">
<h3 id="orgd38d1f4"><span class="section-number-3">1.9</span> Template for has/read/write the dataset of numerical data</h3>
<div id="outline-container-orgaddba62" class="outline-3">
<h3 id="orgaddba62"><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.
@ -1110,8 +1103,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org4ee4f98" class="outline-3">
<h3 id="org4ee4f98"><span class="section-number-3">1.10</span> Template for has/read/write the dataset of strings</h3>
<div id="outline-container-org2a2ef3e" class="outline-3">
<h3 id="org2a2ef3e"><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.
@ -1212,8 +1205,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orge83df4c" class="outline-3">
<h3 id="orge83df4c"><span class="section-number-3">1.11</span> Template for has/read/write the string attribute</h3>
<div id="outline-container-orgfca58bb" class="outline-3">
<h3 id="orgfca58bb"><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>
@ -1287,8 +1280,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org71ffd4f" class="outline-3">
<h3 id="org71ffd4f"><span class="section-number-3">1.12</span> Template for has/read/write the dataset of sparse data</h3>
<div id="outline-container-org2ca6733" class="outline-3">
<h3 id="org2ca6733"><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
@ -1565,7 +1558,7 @@ 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: 2021-12-17 Fri 16:14</p>
<p class="date">Created: 2021-12-23 Thu 17:22</p>
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<title>TREX Configuration file</title>
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<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgd2dc4f9">1. Metadata (metadata group)</a></li>
<li><a href="#orgdaa99a8">2. Electron (electron group)</a></li>
<li><a href="#org29f1fd5">3. Nucleus (nucleus group)</a></li>
<li><a href="#org276b1f9">4. Effective core potentials (ecp group)</a>
<li><a href="#org6b8a3d1">1. Metadata (metadata group)</a></li>
<li><a href="#orgef9af61">2. Electron (electron group)</a></li>
<li><a href="#org0a221c9">3. Nucleus (nucleus group)</a></li>
<li><a href="#orgfcd80c0">4. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org271f4aa">4.1. Example</a></li>
<li><a href="#orgedfba58">4.1. Example</a></li>
</ul>
</li>
<li><a href="#org309a163">5. Basis set (basis group)</a>
<li><a href="#org742eaea">5. Basis set (basis group)</a>
<ul>
<li><a href="#org404d6e3">5.1. Example</a></li>
<li><a href="#orgfb157ee">5.1. Example</a></li>
</ul>
</li>
<li><a href="#orga3ce8a9">6. Atomic orbitals (ao group)</a>
<li><a href="#org29f8d4c">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="#orgdff4a60">7. Molecular orbitals (mo group)</a>
<li><a href="#orgecb211a">7. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#orga81c8db">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgcf3f1ee">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#orga6753be">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org88f2675">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#orgec590d1">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#org80e8789">9. Reduced density matrices (rdm group)</a></li>
<li><a href="#org9ae4cf9">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#org5cec2e2">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-orgd2dc4f9" class="outline-2">
<h2 id="orgd2dc4f9"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org6b8a3d1" class="outline-2">
<h2 id="org6b8a3d1"><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="orge8de5b9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org52e5314" 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-orgdaa99a8" class="outline-2">
<h2 id="orgdaa99a8"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div id="outline-container-orgef9af61" class="outline-2">
<h2 id="orgef9af61"><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="org48808a6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb6215e5" 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-org29f1fd5" class="outline-2">
<h2 id="org29f1fd5"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div id="outline-container-org0a221c9" class="outline-2">
<h2 id="org0a221c9"><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="org6b8fe1d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org9606555" 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-org276b1f9" class="outline-2">
<h2 id="org276b1f9"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div id="outline-container-orgfcd80c0" class="outline-2">
<h2 id="orgfcd80c0"><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="orged79c36" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org3356398" 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-org271f4aa" class="outline-3">
<h3 id="org271f4aa"><span class="section-number-3">4.1</span> Example</h3>
<div id="outline-container-orgedfba58" class="outline-3">
<h3 id="orgedfba58"><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-org309a163" class="outline-2">
<h2 id="org309a163"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div id="outline-container-org742eaea" class="outline-2">
<h2 id="org742eaea"><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="orgdff4428" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org67b2166" 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-org404d6e3" class="outline-3">
<h3 id="org404d6e3"><span class="section-number-3">5.1</span> Example</h3>
<div id="outline-container-orgfb157ee" class="outline-3">
<h3 id="orgfb157ee"><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-orga3ce8a9" class="outline-2">
<h2 id="orga3ce8a9"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div id="outline-container-org29f8d4c" class="outline-2">
<h2 id="org29f8d4c"><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
@ -1081,13 +1081,13 @@ shell, as in the GAMESS convention where
<p>
In such a case, one should set the normalization of the shell (in
the <a href="#org309a163">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#org742eaea">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="orgd5e5519" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org022bcbd" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1139,8 +1139,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
</table>
</div>
<div id="outline-container-org9bbd0b8" class="outline-3">
<h3 id="ao_one_e"><a id="org9bbd0b8"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div id="outline-container-org9169f70" class="outline-3">
<h3 id="ao_one_e"><a id="org9169f70"></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 +1158,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="orgfa84965" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org124e1b5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1225,8 +1225,8 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org9fd7389" class="outline-3">
<h3 id="ao_two_e"><a id="org9fd7389"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div id="outline-container-org02078a0" class="outline-3">
<h3 id="ao_two_e"><a id="org02078a0"></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 +1247,7 @@ notation.
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
</ul>
<table id="org36bcc3a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org4e63750" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1287,10 +1287,10 @@ notation.
</div>
</div>
<div id="outline-container-orgdff4a60" class="outline-2">
<h2 id="orgdff4a60"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div id="outline-container-orgecb211a" class="outline-2">
<h2 id="orgecb211a"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div class="outline-text-2" id="text-7">
<table id="orgf1a8164" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org8613747" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1356,8 +1356,8 @@ notation.
</table>
</div>
<div id="outline-container-orga81c8db" class="outline-3">
<h3 id="orga81c8db"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div id="outline-container-orga6753be" class="outline-3">
<h3 id="orga6753be"><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 +1365,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="orga769fa0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5ba9639" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1432,8 +1432,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-orgcf3f1ee" class="outline-3">
<h3 id="orgcf3f1ee"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div id="outline-container-org88f2675" class="outline-3">
<h3 id="org88f2675"><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 +1441,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org214e7ba" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org97e5807" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1481,13 +1481,13 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-orgec590d1" class="outline-2">
<h2 id="orgec590d1"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
<div id="outline-container-org9ae4cf9" class="outline-2">
<h2 id="org9ae4cf9"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
</div>
<div id="outline-container-org80e8789" class="outline-2">
<h2 id="org80e8789"><span class="section-number-2">9</span> Reduced density matrices (rdm group)</h2>
<div id="outline-container-org5cec2e2" class="outline-2">
<h2 id="org5cec2e2"><span class="section-number-2">9</span> Reduced density matrices (rdm group)</h2>
<div class="outline-text-2" id="text-9">
<table id="orgb582c17" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org72d3eb8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1563,7 +1563,7 @@ the basis of molecular orbitals.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2021-12-17 Fri 16:14</p>
<p class="date">Created: 2021-12-23 Thu 17:22</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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