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README.html
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<title>TREXIO source code documentation</title>
@ -347,7 +347,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-01-10 Mon 09:35</p>
<p class="date">Created: 2022-01-10 Mon 18:22</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Examples</title>
@ -333,24 +333,24 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org0b406b3">1. Accessing sparse quantities</a>
<li><a href="#orga76e869">1. Accessing sparse quantities</a>
<ul>
<li><a href="#orgb091721">1.1. Fortran</a>
<li><a href="#org2150eb4">1.1. Fortran</a>
<ul>
<li><a href="#org8f92994">1.1.1. Declare Temporary variables</a></li>
<li><a href="#orga078839">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgd3c4193">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orgb6076c2">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org8fc5d8e">1.1.5. Allocate memory</a></li>
<li><a href="#orga1fc4f1">1.1.6. Read one-electron quantities</a></li>
<li><a href="#org823a5b6">1.1.7. Read two-electron quantities</a>
<li><a href="#org2b110d9">1.1.1. Declare Temporary variables</a></li>
<li><a href="#orgc9a08f6">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orge7dbf75">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orgfe0645c">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org4d734a7">1.1.5. Allocate memory</a></li>
<li><a href="#orgcad2035">1.1.6. Read one-electron quantities</a></li>
<li><a href="#orgb07302f">1.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org45bceeb">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#orgb342ff9">1.1.7.2. Reduced density matrix</a></li>
<li><a href="#orgacbc54e">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#orgd88fc7d">1.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#orge099873">1.1.8. Compute the energy</a></li>
<li><a href="#org544d9b5">1.1.9. Terminate</a></li>
<li><a href="#org8886438">1.1.8. Compute the energy</a></li>
<li><a href="#orgac1647a">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-org0b406b3" class="outline-2">
<h2 id="org0b406b3"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
<div id="outline-container-orga76e869" class="outline-2">
<h2 id="orga76e869"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-orgb091721" class="outline-3">
<h3 id="orgb091721"><span class="section-number-3">1.1</span> Fortran</h3>
<div id="outline-container-org2150eb4" class="outline-3">
<h3 id="org2150eb4"><span class="section-number-3">1.1</span> Fortran</h3>
<div class="outline-text-3" id="text-1-1">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">print_energy</span>
@ -411,8 +411,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org8f92994" class="outline-4">
<h4 id="org8f92994"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org2b110d9" class="outline-4">
<h4 id="org2b110d9"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div class="outline-text-4" id="text-1-1-1">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #228b22;">integer</span> ::<span style="color: #a0522d;"> i, j, k, l, m</span>
@ -427,8 +427,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-orga078839" class="outline-4">
<h4 id="orga078839"><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-orgc9a08f6" class="outline-4">
<h4 id="orgc9a08f6"><span class="section-number-4">1.1.2</span> Obtain the name of the TREXIO file from the command line, and open it for reading</h4>
<div class="outline-text-4" id="text-1-1-2">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">call</span> <span style="color: #0000ff;">getarg</span>(1, filename)
@ -444,8 +444,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-orgd3c4193" class="outline-4">
<h4 id="orgd3c4193"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orge7dbf75" class="outline-4">
<h4 id="orge7dbf75"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div class="outline-text-4" id="text-1-1-3">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_read_nucleus_repulsion(f, E_nn)
@ -459,8 +459,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-orgb6076c2" class="outline-4">
<h4 id="orgb6076c2"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-orgfe0645c" class="outline-4">
<h4 id="orgfe0645c"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div class="outline-text-4" id="text-1-1-4">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_read_mo_num(f, n)
@ -474,8 +474,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-org8fc5d8e" class="outline-4">
<h4 id="org8fc5d8e"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div id="outline-container-org4d734a7" class="outline-4">
<h4 id="org4d734a7"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div class="outline-text-4" id="text-1-1-5">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">allocate</span>( D(n,n), h0(n,n) )
@ -487,8 +487,8 @@ W(:,:,:,:) = 0.d0
</div>
</div>
<div id="outline-container-orga1fc4f1" class="outline-4">
<h4 id="orga1fc4f1"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-orgcad2035" class="outline-4">
<h4 id="orgcad2035"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div class="outline-text-4" id="text-1-1-6">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_has_mo_1e_int_core_hamiltonian(f)
@ -520,8 +520,8 @@ rc = trexio_read_rdm_1e(f, D)
</div>
</div>
<div id="outline-container-org823a5b6" class="outline-4">
<h4 id="org823a5b6"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-orgb07302f" class="outline-4">
<h4 id="orgb07302f"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div class="outline-text-4" id="text-1-1-7">
<p>
Reading is done with OpenMP. Each thread reads its own buffer, and
@ -537,8 +537,8 @@ to be protected in the critical section when modified.
</p>
</div>
<div id="outline-container-org45bceeb" class="outline-5">
<h5 id="org45bceeb"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-orgacbc54e" class="outline-5">
<h5 id="orgacbc54e"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div class="outline-text-5" id="text-1-1-7-1">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_has_mo_2e_int_eri(f)
@ -587,8 +587,8 @@ icount = BUFSIZE
</div>
</div>
<div id="outline-container-orgb342ff9" class="outline-5">
<h5 id="orgb342ff9"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-orgd88fc7d" class="outline-5">
<h5 id="orgd88fc7d"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div class="outline-text-5" id="text-1-1-7-2">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_has_rdm_2e(f)
@ -632,8 +632,8 @@ icount = bufsize
</div>
</div>
<div id="outline-container-orge099873" class="outline-4">
<h4 id="orge099873"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div id="outline-container-org8886438" class="outline-4">
<h4 id="org8886438"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div class="outline-text-4" id="text-1-1-8">
<p>
When the orbitals are real, we can use
@ -679,8 +679,8 @@ E = E + E_nn
</div>
</div>
<div id="outline-container-org544d9b5" class="outline-4">
<h4 id="org544d9b5"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div id="outline-container-orgac1647a" class="outline-4">
<h4 id="orgac1647a"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div class="outline-text-4" id="text-1-1-9">
<div class="org-src-container">
<pre class="src src-f90"> <span style="color: #a020f0;">deallocate</span>( D, h0, G, W )
@ -695,7 +695,7 @@ E = E + E_nn
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-01-10 Mon 09:35</p>
<p class="date">Created: 2022-01-10 Mon 18:22</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-01-10 Mon 09:35 -->
<!-- 2022-01-10 Mon 18:22 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title>
@ -347,7 +347,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-01-10 Mon 09:35</p>
<p class="date">Created: 2022-01-10 Mon 18:22</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-01-10 Mon 09:35 -->
<!-- 2022-01-10 Mon 18:22 -->
<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>
@ -333,131 +333,131 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org956c50b">1. Coding conventions</a>
<li><a href="#orgbed1e14">1. Coding conventions</a>
<ul>
<li><a href="#orgd047d12">1.1. Memory allocation</a></li>
<li><a href="#orgf823e37">1.1. Memory allocation</a></li>
</ul>
</li>
<li><a href="#org266e708">2. Front end</a>
<li><a href="#orgc27a865">2. Front end</a>
<ul>
<li><a href="#org4702848">2.1. Error handling</a>
<li><a href="#orgad90405">2.1. Error handling</a>
<ul>
<li><a href="#org7af5543">2.1.1. Decoding errors</a>
<li><a href="#orgb9a6f15">2.1.1. Decoding errors</a>
<ul>
<li><a href="#orgce8fd38">2.1.1.1. C source code</a></li>
<li><a href="#orgf6d3d1d">2.1.1.2. Fortran interface</a></li>
<li><a href="#org768bb02">2.1.1.3. Python interface</a></li>
<li><a href="#org9b40dd4">2.1.1.1. C source code</a></li>
<li><a href="#org5971aa4">2.1.1.2. Fortran interface</a></li>
<li><a href="#org10ccbd0">2.1.1.3. Python interface</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org401626b">2.2. Back ends</a>
<li><a href="#org9a81e85">2.2. Back ends</a>
<ul>
<li><a href="#org77a8ba8">2.2.1. C</a></li>
<li><a href="#org86ec0a6">2.2.2. Fortran</a></li>
<li><a href="#org9aa146f">2.2.3. Python</a></li>
<li><a href="#org58476f0">2.2.1. C</a></li>
<li><a href="#org3940fb3">2.2.2. Fortran</a></li>
<li><a href="#org3fb8315">2.2.3. Python</a></li>
</ul>
</li>
<li><a href="#org7192c2b">2.3. Read/write behavior</a></li>
<li><a href="#org0bee8ad">2.4. TREXIO file type</a>
<li><a href="#org7e99adc">2.3. Read/write behavior</a></li>
<li><a href="#org6cdb48c">2.4. TREXIO file type</a>
<ul>
<li><a href="#orgcda5c4e">2.4.1. TREXIO<sub>File</sub> Python class</a></li>
<li><a href="#orgad74548">2.4.1. TREXIO<sub>File</sub> Python class</a></li>
</ul>
</li>
<li><a href="#orgbc85238">2.5. Polymorphism of the file handle</a></li>
<li><a href="#orgfbfdf7a">2.6. File opening</a>
<li><a href="#org9cc7c79">2.5. Polymorphism of the file handle</a></li>
<li><a href="#orga5b8c60">2.6. File opening</a>
<ul>
<li><a href="#org32849f3">2.6.1. C</a></li>
<li><a href="#org96849f4">2.6.2. Fortran</a></li>
<li><a href="#orgf1469b2">2.6.3. Python</a></li>
<li><a href="#orgdaa8953">2.6.4. Zero-based versus one-based arrays of indices</a></li>
<li><a href="#orgfa13268">2.6.1. C</a></li>
<li><a href="#org8e6852c">2.6.2. Fortran</a></li>
<li><a href="#org0ab91fd">2.6.3. Python</a></li>
<li><a href="#org7fea51d">2.6.4. Zero-based versus one-based arrays of indices</a></li>
</ul>
</li>
<li><a href="#org663218e">2.7. File closing</a>
<li><a href="#org9e9cc16">2.7. File closing</a>
<ul>
<li><a href="#org940c8cd">2.7.1. C</a></li>
<li><a href="#orgd03fc36">2.7.2. Fortran</a></li>
<li><a href="#orgfc0984f">2.7.3. Python</a></li>
<li><a href="#org95d4bcb">2.7.1. C</a></li>
<li><a href="#org04ad115">2.7.2. Fortran</a></li>
<li><a href="#org1630e80">2.7.3. Python</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgacf8d29">3. Templates for front end</a>
<li><a href="#orgbcfe051">3. Templates for front end</a>
<ul>
<li><a href="#org30bf8ed">3.1. Description</a></li>
<li><a href="#orgcbc5d15">3.2. Templates for front end has/read/write a single numerical attribute</a>
<li><a href="#orgca6fa47">3.1. Description</a></li>
<li><a href="#org1d8d99c">3.2. Templates for front end has/read/write a single numerical attribute</a>
<ul>
<li><a href="#orgef87da5">3.2.1. Introduction</a></li>
<li><a href="#orgca9736d">3.2.2. C templates for front end</a>
<li><a href="#org5c326d3">3.2.1. Introduction</a></li>
<li><a href="#org5141c93">3.2.2. C templates for front end</a>
<ul>
<li><a href="#org48f1573">3.2.2.1. Function declarations</a></li>
<li><a href="#org10c0ae7">3.2.2.2. Source code for double precision functions</a></li>
<li><a href="#org7a07bc6">3.2.2.3. Source code for single precision functions</a></li>
<li><a href="#org1c98953">3.2.2.4. Source code for default functions</a></li>
<li><a href="#org6bc8636">3.2.2.1. Function declarations</a></li>
<li><a href="#org0e13653">3.2.2.2. Source code for double precision functions</a></li>
<li><a href="#orge923518">3.2.2.3. Source code for single precision functions</a></li>
<li><a href="#org6f44be1">3.2.2.4. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#orgdb7dc4e">3.2.3. Fortran templates for front end</a></li>
<li><a href="#orgfe627ff">3.2.4. Python templates for front end</a></li>
<li><a href="#org8b684b1">3.2.3. Fortran templates for front end</a></li>
<li><a href="#org2d7e9df">3.2.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#org9ce9571">3.3. Templates for front end has/read/write a dataset of numerical data</a>
<li><a href="#orgf4eb565">3.3. Templates for front end has/read/write a dataset of numerical data</a>
<ul>
<li><a href="#orgce5fea6">3.3.1. Introduction</a></li>
<li><a href="#org01bde3f">3.3.2. C templates for front end</a>
<li><a href="#org1d31cce">3.3.1. Introduction</a></li>
<li><a href="#orgcd8bcca">3.3.2. C templates for front end</a>
<ul>
<li><a href="#org737924f">3.3.2.1. Function declarations</a></li>
<li><a href="#org93644d4">3.3.2.2. Source code for double precision functions</a></li>
<li><a href="#org9b2733f">3.3.2.3. Source code for single precision functions</a></li>
<li><a href="#orga3a081c">3.3.2.4. Source code for memory-safe functions</a></li>
<li><a href="#orgab2e8c1">3.3.2.5. Source code for default functions</a></li>
<li><a href="#org58c0320">3.3.2.1. Function declarations</a></li>
<li><a href="#org9875203">3.3.2.2. Source code for double precision functions</a></li>
<li><a href="#orge787734">3.3.2.3. Source code for single precision functions</a></li>
<li><a href="#orgd38571a">3.3.2.4. Source code for memory-safe functions</a></li>
<li><a href="#org7b68abc">3.3.2.5. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#org1109900">3.3.3. Fortran templates for front end</a></li>
<li><a href="#org6e3fefb">3.3.4. Python templates for front end</a></li>
<li><a href="#org469432f">3.3.3. Fortran templates for front end</a></li>
<li><a href="#org9b002fd">3.3.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#orge93fdcb">3.4. Templates for front end has/read/write a dataset of sparse data</a>
<li><a href="#org1b5bb3b">3.4. Templates for front end has/read/write a dataset of sparse data</a>
<ul>
<li><a href="#orgba927dc">3.4.1. Introduction</a></li>
<li><a href="#org26c0215">3.4.2. C templates for front end</a>
<li><a href="#org474d697">3.4.1. Introduction</a></li>
<li><a href="#org0f937af">3.4.2. C templates for front end</a>
<ul>
<li><a href="#org9194050">3.4.2.1. Function declarations</a></li>
<li><a href="#org2e7c11b">3.4.2.2. Source code for default functions</a></li>
<li><a href="#orgcbe1ef5">3.4.2.1. Function declarations</a></li>
<li><a href="#orgac81ace">3.4.2.2. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#org6afda80">3.4.3. Fortran templates for front end</a></li>
<li><a href="#org65e1ef6">3.4.4. Python templates for front end</a></li>
<li><a href="#orge0a4a3e">3.4.3. Fortran templates for front end</a></li>
<li><a href="#org7aee096">3.4.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#org6089008">3.5. Templates for front end has/read/write a dataset of strings</a>
<li><a href="#org8126a75">3.5. Templates for front end has/read/write a dataset of strings</a>
<ul>
<li><a href="#org6dee37a">3.5.1. Introduction</a></li>
<li><a href="#org1783e7a">3.5.2. C templates for front end</a>
<li><a href="#org255d2d1">3.5.1. Introduction</a></li>
<li><a href="#org381d730">3.5.2. C templates for front end</a>
<ul>
<li><a href="#orga4fac9e">3.5.2.1. Function declarations</a></li>
<li><a href="#org8d1fc81">3.5.2.2. Source code for default functions</a></li>
<li><a href="#org0744081">3.5.2.1. Function declarations</a></li>
<li><a href="#org7022530">3.5.2.2. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#orgf25a3e0">3.5.3. Fortran templates for front end</a></li>
<li><a href="#org72ce31f">3.5.4. Python templates for front end</a></li>
<li><a href="#org52b1064">3.5.3. Fortran templates for front end</a></li>
<li><a href="#org2b0ba73">3.5.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#org3e2af42">3.6. Templates for front end has/read/write a single string attribute</a>
<li><a href="#org099c527">3.6. Templates for front end has/read/write a single string attribute</a>
<ul>
<li><a href="#org42598ae">3.6.1. Introduction</a></li>
<li><a href="#orge24aac0">3.6.2. C templates for front end</a>
<li><a href="#org107cef1">3.6.1. Introduction</a></li>
<li><a href="#org738e7f8">3.6.2. C templates for front end</a>
<ul>
<li><a href="#org67157bd">3.6.2.1. Function declarations</a></li>
<li><a href="#orgd3db94a">3.6.2.2. Source code for default functions</a></li>
<li><a href="#orgd24dc02">3.6.2.1. Function declarations</a></li>
<li><a href="#org3911c38">3.6.2.2. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#orgaa49a67">3.6.3. Fortran templates for front end</a></li>
<li><a href="#orgb2e4203">3.6.4. Python templates for front end</a></li>
<li><a href="#org64cb15f">3.6.3. Fortran templates for front end</a></li>
<li><a href="#org4a8f231">3.6.4. Python templates for front end</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org0342021">4. Fortran helper/wrapper functions</a></li>
<li><a href="#org92f03ed">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-org956c50b" class="outline-2">
<h2 id="org956c50b"><span class="section-number-2">1</span> Coding conventions</h2>
<div id="outline-container-orgbed1e14" class="outline-2">
<h2 id="orgbed1e14"><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-orgd047d12" class="outline-3">
<h3 id="orgd047d12"><span class="section-number-3">1.1</span> Memory allocation</h3>
<div id="outline-container-orgf823e37" class="outline-3">
<h3 id="orgf823e37"><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-org266e708" class="outline-2">
<h2 id="org266e708"><span class="section-number-2">2</span> Front end</h2>
<div id="outline-container-orgc27a865" class="outline-2">
<h2 id="orgc27a865"><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-org4702848" class="outline-3">
<h3 id="org4702848"><span class="section-number-3">2.1</span> Error handling</h3>
<div id="outline-container-orgad90405" class="outline-3">
<h3 id="orgad90405"><span class="section-number-3">2.1</span> Error handling</h3>
<div class="outline-text-3" id="text-2-1">
<table id="orgfae716d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga8e0718" 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-org7af5543" class="outline-4">
<h4 id="org7af5543"><span class="section-number-4">2.1.1</span> Decoding errors</h4>
<div id="outline-container-orgb9a6f15" class="outline-4">
<h4 id="orgb9a6f15"><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-orgce8fd38" class="outline-5">
<h5 id="orgce8fd38"><span class="section-number-5">2.1.1.1</span> C source code</h5>
<div id="outline-container-org9b40dd4" class="outline-5">
<h5 id="org9b40dd4"><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-orgf6d3d1d" class="outline-5">
<h5 id="orgf6d3d1d"><span class="section-number-5">2.1.1.2</span> Fortran interface</h5>
<div id="outline-container-org5971aa4" class="outline-5">
<h5 id="org5971aa4"><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-org768bb02" class="outline-5">
<h5 id="org768bb02"><span class="section-number-5">2.1.1.3</span> Python interface</h5>
<div id="outline-container-org10ccbd0" class="outline-5">
<h5 id="org10ccbd0"><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-org401626b" class="outline-3">
<h3 id="org401626b"><span class="section-number-3">2.2</span> Back ends</h3>
<div id="outline-container-org9a81e85" class="outline-3">
<h3 id="org9a81e85"><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-org77a8ba8" class="outline-4">
<h4 id="org77a8ba8"><span class="section-number-4">2.2.1</span> C</h4>
<div id="outline-container-org58476f0" class="outline-4">
<h4 id="org58476f0"><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-org86ec0a6" class="outline-4">
<h4 id="org86ec0a6"><span class="section-number-4">2.2.2</span> Fortran</h4>
<div id="outline-container-org3940fb3" class="outline-4">
<h4 id="org3940fb3"><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-org9aa146f" class="outline-4">
<h4 id="org9aa146f"><span class="section-number-4">2.2.3</span> Python</h4>
<div id="outline-container-org3fb8315" class="outline-4">
<h4 id="org3fb8315"><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-org7192c2b" class="outline-3">
<h3 id="org7192c2b"><span class="section-number-3">2.3</span> Read/write behavior</h3>
<div id="outline-container-org7e99adc" class="outline-3">
<h3 id="org7e99adc"><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-org0bee8ad" class="outline-3">
<h3 id="org0bee8ad"><span class="section-number-3">2.4</span> TREXIO file type</h3>
<div id="outline-container-org6cdb48c" class="outline-3">
<h3 id="org6cdb48c"><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-orgcda5c4e" class="outline-4">
<h4 id="orgcda5c4e"><span class="section-number-4">2.4.1</span> TREXIO<sub>File</sub> Python class</h4>
<div id="outline-container-orgad74548" class="outline-4">
<h4 id="orgad74548"><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-orgbc85238" class="outline-3">
<h3 id="orgbc85238"><span class="section-number-3">2.5</span> Polymorphism of the file handle</h3>
<div id="outline-container-org9cc7c79" class="outline-3">
<h3 id="org9cc7c79"><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-orgfbfdf7a" class="outline-3">
<h3 id="orgfbfdf7a"><span class="section-number-3">2.6</span> File opening</h3>
<div id="outline-container-orga5b8c60" class="outline-3">
<h3 id="orga5b8c60"><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-org32849f3" class="outline-4">
<h4 id="org32849f3"><span class="section-number-4">2.6.1</span> C</h4>
<div id="outline-container-orgfa13268" class="outline-4">
<h4 id="orgfa13268"><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-org96849f4" class="outline-4">
<h4 id="org96849f4"><span class="section-number-4">2.6.2</span> Fortran</h4>
<div id="outline-container-org8e6852c" class="outline-4">
<h4 id="org8e6852c"><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-orgf1469b2" class="outline-4">
<h4 id="orgf1469b2"><span class="section-number-4">2.6.3</span> Python</h4>
<div id="outline-container-org0ab91fd" class="outline-4">
<h4 id="org0ab91fd"><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-orgdaa8953" class="outline-4">
<h4 id="orgdaa8953"><span class="section-number-4">2.6.4</span> Zero-based versus one-based arrays of indices</h4>
<div id="outline-container-org7fea51d" class="outline-4">
<h4 id="org7fea51d"><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-org663218e" class="outline-3">
<h3 id="org663218e"><span class="section-number-3">2.7</span> File closing</h3>
<div id="outline-container-org9e9cc16" class="outline-3">
<h3 id="org9e9cc16"><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-org940c8cd" class="outline-4">
<h4 id="org940c8cd"><span class="section-number-4">2.7.1</span> C</h4>
<div id="outline-container-org95d4bcb" class="outline-4">
<h4 id="org95d4bcb"><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-orgd03fc36" class="outline-4">
<h4 id="orgd03fc36"><span class="section-number-4">2.7.2</span> Fortran</h4>
<div id="outline-container-org04ad115" class="outline-4">
<h4 id="org04ad115"><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-orgfc0984f" class="outline-4">
<h4 id="orgfc0984f"><span class="section-number-4">2.7.3</span> Python</h4>
<div id="outline-container-org1630e80" class="outline-4">
<h4 id="org1630e80"><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-orgacf8d29" class="outline-2">
<h2 id="orgacf8d29"><span class="section-number-2">3</span> Templates for front end</h2>
<div id="outline-container-orgbcfe051" class="outline-2">
<h2 id="orgbcfe051"><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-org30bf8ed" class="outline-3">
<h3 id="org30bf8ed"><span class="section-number-3">3.1</span> Description</h3>
<div id="outline-container-orgca6fa47" class="outline-3">
<h3 id="orgca6fa47"><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-orgcbc5d15" class="outline-3">
<h3 id="orgcbc5d15"><span class="section-number-3">3.2</span> Templates for front end has/read/write a single numerical attribute</h3>
<div id="outline-container-org1d8d99c" class="outline-3">
<h3 id="org1d8d99c"><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-orgef87da5" class="outline-4">
<h4 id="orgef87da5"><span class="section-number-4">3.2.1</span> Introduction</h4>
<div id="outline-container-org5c326d3" class="outline-4">
<h4 id="org5c326d3"><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-orgca9736d" class="outline-4">
<h4 id="orgca9736d"><span class="section-number-4">3.2.2</span> C templates for front end</h4>
<div id="outline-container-org5141c93" class="outline-4">
<h4 id="org5141c93"><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-org48f1573" class="outline-5">
<h5 id="org48f1573"><span class="section-number-5">3.2.2.1</span> Function declarations</h5>
<div id="outline-container-org6bc8636" class="outline-5">
<h5 id="org6bc8636"><span class="section-number-5">3.2.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-org10c0ae7" class="outline-5">
<h5 id="org10c0ae7"><span class="section-number-5">3.2.2.2</span> Source code for double precision functions</h5>
<div id="outline-container-org0e13653" class="outline-5">
<h5 id="org0e13653"><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-org7a07bc6" class="outline-5">
<h5 id="org7a07bc6"><span class="section-number-5">3.2.2.3</span> Source code for single precision functions</h5>
<div id="outline-container-orge923518" class="outline-5">
<h5 id="orge923518"><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-org1c98953" class="outline-5">
<h5 id="org1c98953"><span class="section-number-5">3.2.2.4</span> Source code for default functions</h5>
<div id="outline-container-org6f44be1" class="outline-5">
<h5 id="org6f44be1"><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-orgdb7dc4e" class="outline-4">
<h4 id="orgdb7dc4e"><span class="section-number-4">3.2.3</span> Fortran templates for front end</h4>
<div id="outline-container-org8b684b1" class="outline-4">
<h4 id="org8b684b1"><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-orgfe627ff" class="outline-4">
<h4 id="orgfe627ff"><span class="section-number-4">3.2.4</span> Python templates for front end</h4>
<div id="outline-container-org2d7e9df" class="outline-4">
<h4 id="org2d7e9df"><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-org9ce9571" class="outline-3">
<h3 id="org9ce9571"><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-orgf4eb565" class="outline-3">
<h3 id="orgf4eb565"><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-orgce5fea6" class="outline-4">
<h4 id="orgce5fea6"><span class="section-number-4">3.3.1</span> Introduction</h4>
<div id="outline-container-org1d31cce" class="outline-4">
<h4 id="org1d31cce"><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-org01bde3f" class="outline-4">
<h4 id="org01bde3f"><span class="section-number-4">3.3.2</span> C templates for front end</h4>
<div id="outline-container-orgcd8bcca" class="outline-4">
<h4 id="orgcd8bcca"><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-org737924f" class="outline-5">
<h5 id="org737924f"><span class="section-number-5">3.3.2.1</span> Function declarations</h5>
<div id="outline-container-org58c0320" class="outline-5">
<h5 id="org58c0320"><span class="section-number-5">3.3.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-org93644d4" class="outline-5">
<h5 id="org93644d4"><span class="section-number-5">3.3.2.2</span> Source code for double precision functions</h5>
<div id="outline-container-org9875203" class="outline-5">
<h5 id="org9875203"><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-org9b2733f" class="outline-5">
<h5 id="org9b2733f"><span class="section-number-5">3.3.2.3</span> Source code for single precision functions</h5>
<div id="outline-container-orge787734" class="outline-5">
<h5 id="orge787734"><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-orga3a081c" class="outline-5">
<h5 id="orga3a081c"><span class="section-number-5">3.3.2.4</span> Source code for memory-safe functions</h5>
<div id="outline-container-orgd38571a" class="outline-5">
<h5 id="orgd38571a"><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="orgf2ac2f7"><span style="color: #228b22;">trexio_exit_code</span> <span style="color: #a0522d;">rc</span>;
<pre class="src src-c" id="org1be02b0"><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-orgab2e8c1" class="outline-5">
<h5 id="orgab2e8c1"><span class="section-number-5">3.3.2.5</span> Source code for default functions</h5>
<div id="outline-container-org7b68abc" class="outline-5">
<h5 id="org7b68abc"><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-org1109900" class="outline-4">
<h4 id="org1109900"><span class="section-number-4">3.3.3</span> Fortran templates for front end</h4>
<div id="outline-container-org469432f" class="outline-4">
<h4 id="org469432f"><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-org6e3fefb" class="outline-4">
<h4 id="org6e3fefb"><span class="section-number-4">3.3.4</span> Python templates for front end</h4>
<div id="outline-container-org9b002fd" class="outline-4">
<h4 id="org9b002fd"><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-orge93fdcb" class="outline-3">
<h3 id="orge93fdcb"><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-org1b5bb3b" class="outline-3">
<h3 id="org1b5bb3b"><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-orgba927dc" class="outline-4">
<h4 id="orgba927dc"><span class="section-number-4">3.4.1</span> Introduction</h4>
<div id="outline-container-org474d697" class="outline-4">
<h4 id="org474d697"><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-org26c0215" class="outline-4">
<h4 id="org26c0215"><span class="section-number-4">3.4.2</span> C templates for front end</h4>
<div id="outline-container-org0f937af" class="outline-4">
<h4 id="org0f937af"><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-org9194050" class="outline-5">
<h5 id="org9194050"><span class="section-number-5">3.4.2.1</span> Function declarations</h5>
<div id="outline-container-orgcbe1ef5" class="outline-5">
<h5 id="orgcbe1ef5"><span class="section-number-5">3.4.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-org2e7c11b" class="outline-5">
<h5 id="org2e7c11b"><span class="section-number-5">3.4.2.2</span> Source code for default functions</h5>
<div id="outline-container-orgac81ace" class="outline-5">
<h5 id="orgac81ace"><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-org6afda80" class="outline-4">
<h4 id="org6afda80"><span class="section-number-4">3.4.3</span> Fortran templates for front end</h4>
<div id="outline-container-orge0a4a3e" class="outline-4">
<h4 id="orge0a4a3e"><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-org65e1ef6" class="outline-4">
<h4 id="org65e1ef6"><span class="section-number-4">3.4.4</span> Python templates for front end</h4>
<div id="outline-container-org7aee096" class="outline-4">
<h4 id="org7aee096"><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-org6089008" class="outline-3">
<h3 id="org6089008"><span class="section-number-3">3.5</span> Templates for front end has/read/write a dataset of strings</h3>
<div id="outline-container-org8126a75" class="outline-3">
<h3 id="org8126a75"><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-org6dee37a" class="outline-4">
<h4 id="org6dee37a"><span class="section-number-4">3.5.1</span> Introduction</h4>
<div id="outline-container-org255d2d1" class="outline-4">
<h4 id="org255d2d1"><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-org1783e7a" class="outline-4">
<h4 id="org1783e7a"><span class="section-number-4">3.5.2</span> C templates for front end</h4>
<div id="outline-container-org381d730" class="outline-4">
<h4 id="org381d730"><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-orga4fac9e" class="outline-5">
<h5 id="orga4fac9e"><span class="section-number-5">3.5.2.1</span> Function declarations</h5>
<div id="outline-container-org0744081" class="outline-5">
<h5 id="org0744081"><span class="section-number-5">3.5.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-org8d1fc81" class="outline-5">
<h5 id="org8d1fc81"><span class="section-number-5">3.5.2.2</span> Source code for default functions</h5>
<div id="outline-container-org7022530" class="outline-5">
<h5 id="org7022530"><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-orgf25a3e0" class="outline-4">
<h4 id="orgf25a3e0"><span class="section-number-4">3.5.3</span> Fortran templates for front end</h4>
<div id="outline-container-org52b1064" class="outline-4">
<h4 id="org52b1064"><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-org72ce31f" class="outline-4">
<h4 id="org72ce31f"><span class="section-number-4">3.5.4</span> Python templates for front end</h4>
<div id="outline-container-org2b0ba73" class="outline-4">
<h4 id="org2b0ba73"><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-org3e2af42" class="outline-3">
<h3 id="org3e2af42"><span class="section-number-3">3.6</span> Templates for front end has/read/write a single string attribute</h3>
<div id="outline-container-org099c527" class="outline-3">
<h3 id="org099c527"><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-org42598ae" class="outline-4">
<h4 id="org42598ae"><span class="section-number-4">3.6.1</span> Introduction</h4>
<div id="outline-container-org107cef1" class="outline-4">
<h4 id="org107cef1"><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-orge24aac0" class="outline-4">
<h4 id="orge24aac0"><span class="section-number-4">3.6.2</span> C templates for front end</h4>
<div id="outline-container-org738e7f8" class="outline-4">
<h4 id="org738e7f8"><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-org67157bd" class="outline-5">
<h5 id="org67157bd"><span class="section-number-5">3.6.2.1</span> Function declarations</h5>
<div id="outline-container-orgd24dc02" class="outline-5">
<h5 id="orgd24dc02"><span class="section-number-5">3.6.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-orgd3db94a" class="outline-5">
<h5 id="orgd3db94a"><span class="section-number-5">3.6.2.2</span> Source code for default functions</h5>
<div id="outline-container-org3911c38" class="outline-5">
<h5 id="org3911c38"><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-orgaa49a67" class="outline-4">
<h4 id="orgaa49a67"><span class="section-number-4">3.6.3</span> Fortran templates for front end</h4>
<div id="outline-container-org64cb15f" class="outline-4">
<h4 id="org64cb15f"><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-orgb2e4203" class="outline-4">
<h4 id="orgb2e4203"><span class="section-number-4">3.6.4</span> Python templates for front end</h4>
<div id="outline-container-org4a8f231" class="outline-4">
<h4 id="org4a8f231"><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-org0342021" class="outline-2">
<h2 id="org0342021"><span class="section-number-2">4</span> Fortran helper/wrapper functions</h2>
<div id="outline-container-org92f03ed" class="outline-2">
<h2 id="org92f03ed"><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: 2022-01-10 Mon 09:35</p>
<p class="date">Created: 2022-01-10 Mon 18:22</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>
<!-- 2022-01-10 Mon 09:35 -->
<!-- 2022-01-10 Mon 18:22 -->
<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="#org218cb2b">1. HDF5 back end</a>
<li><a href="#orgc38e664">1. HDF5 back end</a>
<ul>
<li><a href="#org59e8d8b">1.1. Template for HDF5 definitions</a></li>
<li><a href="#orga369a3a">1.2. Template for HDF5 structures</a></li>
<li><a href="#orged1a613">1.3. Template for HDF5 init/deinit</a></li>
<li><a href="#org667cfaa">1.4. Template for HDF5 has/read/write the numerical attribute</a></li>
<li><a href="#org60fcb4d">1.5. Template for HDF5 has/read/write the dataset of numerical data</a></li>
<li><a href="#org76f96af">1.6. Template for HDF5 has/read/write the dataset of sparse data</a></li>
<li><a href="#org8a1eb01">1.7. Template for HDF5 has/read/write the dataset of strings</a></li>
<li><a href="#orgcb0b0d7">1.8. Template for HDF5 has/read/write the string attribute</a></li>
<li><a href="#orgd5d942d">1.9. Helper functions</a></li>
<li><a href="#org9e8a6d4">1.1. Template for HDF5 definitions</a></li>
<li><a href="#orgd9e7165">1.2. Template for HDF5 structures</a></li>
<li><a href="#org5806349">1.3. Template for HDF5 init/deinit</a></li>
<li><a href="#org78bb760">1.4. Template for HDF5 has/read/write the numerical attribute</a></li>
<li><a href="#orgedb86b6">1.5. Template for HDF5 has/read/write the dataset of numerical data</a></li>
<li><a href="#org5011f72">1.6. Template for HDF5 has/read/write the dataset of sparse data</a></li>
<li><a href="#org7f5217d">1.7. Template for HDF5 has/read/write the dataset of strings</a></li>
<li><a href="#orgbbfb833">1.8. Template for HDF5 has/read/write the string attribute</a></li>
<li><a href="#orgecb320a">1.9. Helper functions</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org218cb2b" class="outline-2">
<h2 id="org218cb2b"><span class="section-number-2">1</span> HDF5 back end</h2>
<div id="outline-container-orgc38e664" class="outline-2">
<h2 id="orgc38e664"><span class="section-number-2">1</span> HDF5 back end</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-org59e8d8b" class="outline-3">
<h3 id="org59e8d8b"><span class="section-number-3">1.1</span> Template for HDF5 definitions</h3>
<div id="outline-container-org9e8a6d4" class="outline-3">
<h3 id="org9e8a6d4"><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-orga369a3a" class="outline-3">
<h3 id="orga369a3a"><span class="section-number-3">1.2</span> Template for HDF5 structures</h3>
<div id="outline-container-orgd9e7165" class="outline-3">
<h3 id="orgd9e7165"><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-orged1a613" class="outline-3">
<h3 id="orged1a613"><span class="section-number-3">1.3</span> Template for HDF5 init/deinit</h3>
<div id="outline-container-org5806349" class="outline-3">
<h3 id="org5806349"><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-org667cfaa" class="outline-3">
<h3 id="org667cfaa"><span class="section-number-3">1.4</span> Template for HDF5 has/read/write the numerical attribute</h3>
<div id="outline-container-org78bb760" class="outline-3">
<h3 id="org78bb760"><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-org60fcb4d" class="outline-3">
<h3 id="org60fcb4d"><span class="section-number-3">1.5</span> Template for HDF5 has/read/write the dataset of numerical data</h3>
<div id="outline-container-orgedb86b6" class="outline-3">
<h3 id="orgedb86b6"><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-org76f96af" class="outline-3">
<h3 id="org76f96af"><span class="section-number-3">1.6</span> Template for HDF5 has/read/write the dataset of sparse data</h3>
<div id="outline-container-org5011f72" class="outline-3">
<h3 id="org5011f72"><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-org8a1eb01" class="outline-3">
<h3 id="org8a1eb01"><span class="section-number-3">1.7</span> Template for HDF5 has/read/write the dataset of strings</h3>
<div id="outline-container-org7f5217d" class="outline-3">
<h3 id="org7f5217d"><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-orgcb0b0d7" class="outline-3">
<h3 id="orgcb0b0d7"><span class="section-number-3">1.8</span> Template for HDF5 has/read/write the string attribute</h3>
<div id="outline-container-orgbbfb833" class="outline-3">
<h3 id="orgbbfb833"><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-orgd5d942d" class="outline-3">
<h3 id="orgd5d942d"><span class="section-number-3">1.9</span> Helper functions</h3>
<div id="outline-container-orgecb320a" class="outline-3">
<h3 id="orgecb320a"><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: 2022-01-10 Mon 09:35</p>
<p class="date">Created: 2022-01-10 Mon 18:22</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>
<!-- 2022-01-10 Mon 09:35 -->
<!-- 2022-01-10 Mon 18:22 -->
<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="#org05d768e">1. TEXT back end</a>
<li><a href="#org4d74ac3">1. TEXT back end</a>
<ul>
<li><a href="#org13eaf28">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#org4d5f841">1.2. Template for general structure in text back end</a></li>
<li><a href="#org74c7f03">1.3. Initialize function (constant part)</a></li>
<li><a href="#orgcb27ff5">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#orgc161140">1.5. Template for text read struct</a></li>
<li><a href="#orgc25416d">1.6. Template for text flush struct</a></li>
<li><a href="#org6f00af9">1.7. Template for text free memory</a></li>
<li><a href="#org27adc0d">1.8. Template for has/read/write the numerical attribute</a></li>
<li><a href="#org453a8c4">1.9. Template for has/read/write the dataset of numerical data</a></li>
<li><a href="#orgc86baf3">1.10. Template for has/read/write the dataset of strings</a></li>
<li><a href="#org2433f62">1.11. Template for has/read/write the string attribute</a></li>
<li><a href="#orgda27417">1.12. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org498effd">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#org8e3d1bf">1.2. Template for general structure in text back end</a></li>
<li><a href="#orgf43bd52">1.3. Initialize function (constant part)</a></li>
<li><a href="#orgeb14bd5">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#orgbc11cde">1.5. Template for text read struct</a></li>
<li><a href="#orgee74ce1">1.6. Template for text flush struct</a></li>
<li><a href="#org1de1316">1.7. Template for text free memory</a></li>
<li><a href="#org71de337">1.8. Template for has/read/write the numerical attribute</a></li>
<li><a href="#orgd40adf2">1.9. Template for has/read/write the dataset of numerical data</a></li>
<li><a href="#org4581123">1.10. Template for has/read/write the dataset of strings</a></li>
<li><a href="#org224cbe7">1.11. Template for has/read/write the string attribute</a></li>
<li><a href="#org8347669">1.12. Template for has/read/write the dataset of sparse data</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org05d768e" class="outline-2">
<h2 id="org05d768e"><span class="section-number-2">1</span> TEXT back end</h2>
<div id="outline-container-org4d74ac3" class="outline-2">
<h2 id="org4d74ac3"><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-org13eaf28" class="outline-3">
<h3 id="org13eaf28"><span class="section-number-3">1.1</span> Template for group-related structures in text back end</h3>
<div id="outline-container-org498effd" class="outline-3">
<h3 id="org498effd"><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-org4d5f841" class="outline-3">
<h3 id="org4d5f841"><span class="section-number-3">1.2</span> Template for general structure in text back end</h3>
<div id="outline-container-org8e3d1bf" class="outline-3">
<h3 id="org8e3d1bf"><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-org74c7f03" class="outline-3">
<h3 id="org74c7f03"><span class="section-number-3">1.3</span> Initialize function (constant part)</h3>
<div id="outline-container-orgf43bd52" class="outline-3">
<h3 id="orgf43bd52"><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-orgcb27ff5" class="outline-3">
<h3 id="orgcb27ff5"><span class="section-number-3">1.4</span> Deinitialize function (templated part)</h3>
<div id="outline-container-orgeb14bd5" class="outline-3">
<h3 id="orgeb14bd5"><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-orgc161140" class="outline-3">
<h3 id="orgc161140"><span class="section-number-3">1.5</span> Template for text read struct</h3>
<div id="outline-container-orgbc11cde" class="outline-3">
<h3 id="orgbc11cde"><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-orgc25416d" class="outline-3">
<h3 id="orgc25416d"><span class="section-number-3">1.6</span> Template for text flush struct</h3>
<div id="outline-container-orgee74ce1" class="outline-3">
<h3 id="orgee74ce1"><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-org6f00af9" class="outline-3">
<h3 id="org6f00af9"><span class="section-number-3">1.7</span> Template for text free memory</h3>
<div id="outline-container-org1de1316" class="outline-3">
<h3 id="org1de1316"><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-org27adc0d" class="outline-3">
<h3 id="org27adc0d"><span class="section-number-3">1.8</span> Template for has/read/write the numerical attribute</h3>
<div id="outline-container-org71de337" class="outline-3">
<h3 id="org71de337"><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-org453a8c4" class="outline-3">
<h3 id="org453a8c4"><span class="section-number-3">1.9</span> Template for has/read/write the dataset of numerical data</h3>
<div id="outline-container-orgd40adf2" class="outline-3">
<h3 id="orgd40adf2"><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-orgc86baf3" class="outline-3">
<h3 id="orgc86baf3"><span class="section-number-3">1.10</span> Template for has/read/write the dataset of strings</h3>
<div id="outline-container-org4581123" class="outline-3">
<h3 id="org4581123"><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-org2433f62" class="outline-3">
<h3 id="org2433f62"><span class="section-number-3">1.11</span> Template for has/read/write the string attribute</h3>
<div id="outline-container-org224cbe7" class="outline-3">
<h3 id="org224cbe7"><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-orgda27417" class="outline-3">
<h3 id="orgda27417"><span class="section-number-3">1.12</span> Template for has/read/write the dataset of sparse data</h3>
<div id="outline-container-org8347669" class="outline-3">
<h3 id="org8347669"><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: 2022-01-10 Mon 09:35</p>
<p class="date">Created: 2022-01-10 Mon 18:22</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

118
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>
<!-- 2022-01-10 Mon 09:35 -->
<!-- 2022-01-10 Mon 18:22 -->
<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="#orgc705fee">1. Metadata (metadata group)</a></li>
<li><a href="#org0e52b03">2. Electron (electron group)</a></li>
<li><a href="#orga5df6dc">3. Nucleus (nucleus group)</a></li>
<li><a href="#org573842a">4. Effective core potentials (ecp group)</a>
<li><a href="#org3129a36">1. Metadata (metadata group)</a></li>
<li><a href="#orgfd97c3d">2. Electron (electron group)</a></li>
<li><a href="#org9074502">3. Nucleus (nucleus group)</a></li>
<li><a href="#org81fe7a3">4. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org66bffcb">4.1. Example</a></li>
<li><a href="#org1417af7">4.1. Example</a></li>
</ul>
</li>
<li><a href="#org679011f">5. Basis set (basis group)</a>
<li><a href="#org965c903">5. Basis set (basis group)</a>
<ul>
<li><a href="#orgc1e84a0">5.1. Example</a></li>
<li><a href="#org1b61de7">5.1. Example</a></li>
</ul>
</li>
<li><a href="#org8c7b545">6. Atomic orbitals (ao group)</a>
<li><a href="#org1f8bb69">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="#orgc189830">7. Molecular orbitals (mo group)</a>
<li><a href="#orgada2ede">7. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#orgfe729c5">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org9be98df">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org3cf74a6">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org73500cf">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#org1b09c8e">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#org72b64fe">9. Reduced density matrices (rdm group)</a></li>
<li><a href="#orgab8c0a6">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#org74ca721">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-orgc705fee" class="outline-2">
<h2 id="orgc705fee"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org3129a36" class="outline-2">
<h2 id="org3129a36"><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="org0544eb8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org1b40b6e" 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-org0e52b03" class="outline-2">
<h2 id="org0e52b03"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div id="outline-container-orgfd97c3d" class="outline-2">
<h2 id="orgfd97c3d"><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="org7c3c29f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgdd3fcde" 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-orga5df6dc" class="outline-2">
<h2 id="orga5df6dc"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div id="outline-container-org9074502" class="outline-2">
<h2 id="org9074502"><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="org9a7ff06" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org48db0ba" 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-org573842a" class="outline-2">
<h2 id="org573842a"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div id="outline-container-org81fe7a3" class="outline-2">
<h2 id="org81fe7a3"><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="org1de6b58" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc34f94b" 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-org66bffcb" class="outline-3">
<h3 id="org66bffcb"><span class="section-number-3">4.1</span> Example</h3>
<div id="outline-container-org1417af7" class="outline-3">
<h3 id="org1417af7"><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-org679011f" class="outline-2">
<h2 id="org679011f"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div id="outline-container-org965c903" class="outline-2">
<h2 id="org965c903"><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="orgabb6837" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org436a11c" 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-orgc1e84a0" class="outline-3">
<h3 id="orgc1e84a0"><span class="section-number-3">5.1</span> Example</h3>
<div id="outline-container-org1b61de7" class="outline-3">
<h3 id="org1b61de7"><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-org8c7b545" class="outline-2">
<h2 id="org8c7b545"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div id="outline-container-org1f8bb69" class="outline-2">
<h2 id="org1f8bb69"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div class="outline-text-2" id="text-6">
<p>
Going from the atomic basis set to AOs implies a systematic
@ -1085,13 +1085,13 @@ shell, as in the GAMESS convention where
<p>
In such a case, one should set the normalization of the shell (in
the <a href="#org679011f">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#org965c903">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="org28a025f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org911d086" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1143,8 +1143,8 @@ introduced here should be \(\frac{\mathcal{N}_{xy}}{\mathcal{N}_{z^2}}\).
</table>
</div>
<div id="outline-container-org453dc82" class="outline-3">
<h3 id="ao_one_e"><a id="org453dc82"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div id="outline-container-orgb3ebf44" class="outline-3">
<h3 id="ao_one_e"><a id="orgb3ebf44"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div class="outline-text-3" id="text-ao_one_e">
<ul class="org-ul">
<li>\[ \hat{V}_{\text{ne}} = \sum_{A=1}^{N_\text{nucl}}
@ -1162,7 +1162,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="orga8bc870" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org184aa9b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1229,8 +1229,8 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-orgc4c1698" class="outline-3">
<h3 id="ao_two_e"><a id="orgc4c1698"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div id="outline-container-org7aa468c" class="outline-3">
<h3 id="ao_two_e"><a id="org7aa468c"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div class="outline-text-3" id="text-ao_two_e">
<p>
The two-electron integrals for a two-electron operator \(\hat{O}\) are
@ -1251,7 +1251,7 @@ notation.
\mathbf{r}_j \vert)}{\vert \mathbf{r}_i - \mathbf{r}_j \vert} \] : electron-electron long range potential</li>
</ul>
<table id="org0d4c9b2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org56d1566" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1291,10 +1291,10 @@ notation.
</div>
</div>
<div id="outline-container-orgc189830" class="outline-2">
<h2 id="orgc189830"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div id="outline-container-orgada2ede" class="outline-2">
<h2 id="orgada2ede"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div class="outline-text-2" id="text-7">
<table id="org86ba407" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org61433e8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1360,8 +1360,8 @@ notation.
</table>
</div>
<div id="outline-container-orgfe729c5" class="outline-3">
<h3 id="orgfe729c5"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div id="outline-container-org3cf74a6" class="outline-3">
<h3 id="org3cf74a6"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div class="outline-text-3" id="text-7-1">
<p>
The operators as the same as those defined in the
@ -1369,7 +1369,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="orgfc7ef6a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5e480ab" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1436,8 +1436,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org9be98df" class="outline-3">
<h3 id="org9be98df"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div id="outline-container-org73500cf" class="outline-3">
<h3 id="org73500cf"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div class="outline-text-3" id="text-7-2">
<p>
The operators as the same as those defined in the
@ -1445,7 +1445,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org2a9179a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org6a0fe09" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1485,11 +1485,11 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org1b09c8e" class="outline-2">
<h2 id="org1b09c8e"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
<div id="outline-container-orgab8c0a6" class="outline-2">
<h2 id="orgab8c0a6"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
</div>
<div id="outline-container-org72b64fe" class="outline-2">
<h2 id="org72b64fe"><span class="section-number-2">9</span> Reduced density matrices (rdm group)</h2>
<div id="outline-container-org74ca721" class="outline-2">
<h2 id="org74ca721"><span class="section-number-2">9</span> Reduced density matrices (rdm group)</h2>
<div class="outline-text-2" id="text-9">
<p>
The reduced density matrices are defined in the basis of molecular
@ -1529,7 +1529,7 @@ components of the two-body density matrix are given by
and the spin-summed one-body density matrix is
\[
\Gamma_{ijkl} = \Gamma_{ijkl}^{\uparrow \uparrow} +
\Gamma_{ijkl}^{\downarrow \downarrow} + \Gamma_{ijkl}^{\uparrow \downarrow}
\Gamma_{ijkl}^{\downarrow \downarrow} + \Gamma_{ijkl}^{\uparrow \downarrow} +
\Gamma_{ijkl}^{\downarrow \uparrow}
\]
</p>
@ -1542,7 +1542,7 @@ The total energy can be computed as:
\]
</p>
<table id="org2efb7f9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga0a0601" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1625,7 +1625,7 @@ The total energy can be computed as:
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-01-10 Mon 09:35</p>
<p class="date">Created: 2022-01-10 Mon 18:22</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>