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README.html
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title>
@ -347,7 +347,7 @@ and bug reports should be submitted at
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-01-07 Fri 17:48</p>
<p class="date">Created: 2022-01-07 Fri 18:41</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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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="#org4b9da87">1. Accessing sparse quantities</a>
<li><a href="#orgaafbe10">1. Accessing sparse quantities</a>
<ul>
<li><a href="#org209a7bd">1.1. Fortran</a>
<li><a href="#org95fcbf4">1.1. Fortran</a>
<ul>
<li><a href="#org33b444e">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org111d6a7">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orge7057c0">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org431517a">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orgb72a65b">1.1.5. Allocate memory</a></li>
<li><a href="#org43f57e7">1.1.6. Read one-electron quantities</a></li>
<li><a href="#org46b91e5">1.1.7. Read two-electron quantities</a>
<li><a href="#org7a738d5">1.1.1. Declare Temporary variables</a></li>
<li><a href="#org31f6867">1.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org2ffe1e6">1.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orgf836c70">1.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org0a54b8a">1.1.5. Allocate memory</a></li>
<li><a href="#org634663f">1.1.6. Read one-electron quantities</a></li>
<li><a href="#orgadfa0ec">1.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#orgc8c29ff">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org345a17b">1.1.7.2. Reduced density matrix</a></li>
<li><a href="#org6fa01c3">1.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org2bb55c9">1.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#orge966447">1.1.8. Compute the energy</a></li>
<li><a href="#orgcb6e0c6">1.1.9. Terminate</a></li>
<li><a href="#org46fe1a8">1.1.8. Compute the energy</a></li>
<li><a href="#org5bd1227">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-org4b9da87" class="outline-2">
<h2 id="org4b9da87"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
<div id="outline-container-orgaafbe10" class="outline-2">
<h2 id="orgaafbe10"><span class="section-number-2">1</span> Accessing sparse quantities</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-org209a7bd" class="outline-3">
<h3 id="org209a7bd"><span class="section-number-3">1.1</span> Fortran</h3>
<div id="outline-container-org95fcbf4" class="outline-3">
<h3 id="org95fcbf4"><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-org33b444e" class="outline-4">
<h4 id="org33b444e"><span class="section-number-4">1.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org7a738d5" class="outline-4">
<h4 id="org7a738d5"><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-org111d6a7" class="outline-4">
<h4 id="org111d6a7"><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-org31f6867" class="outline-4">
<h4 id="org31f6867"><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-orge7057c0" class="outline-4">
<h4 id="orge7057c0"><span class="section-number-4">1.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org2ffe1e6" class="outline-4">
<h4 id="org2ffe1e6"><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-org431517a" class="outline-4">
<h4 id="org431517a"><span class="section-number-4">1.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-orgf836c70" class="outline-4">
<h4 id="orgf836c70"><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-orgb72a65b" class="outline-4">
<h4 id="orgb72a65b"><span class="section-number-4">1.1.5</span> Allocate memory</h4>
<div id="outline-container-org0a54b8a" class="outline-4">
<h4 id="org0a54b8a"><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-org43f57e7" class="outline-4">
<h4 id="org43f57e7"><span class="section-number-4">1.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org634663f" class="outline-4">
<h4 id="org634663f"><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-org46b91e5" class="outline-4">
<h4 id="org46b91e5"><span class="section-number-4">1.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-orgadfa0ec" class="outline-4">
<h4 id="orgadfa0ec"><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-orgc8c29ff" class="outline-5">
<h5 id="orgc8c29ff"><span class="section-number-5">1.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org6fa01c3" class="outline-5">
<h5 id="org6fa01c3"><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-org345a17b" class="outline-5">
<h5 id="org345a17b"><span class="section-number-5">1.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org2bb55c9" class="outline-5">
<h5 id="org2bb55c9"><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-orge966447" class="outline-4">
<h4 id="orge966447"><span class="section-number-4">1.1.8</span> Compute the energy</h4>
<div id="outline-container-org46fe1a8" class="outline-4">
<h4 id="org46fe1a8"><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-orgcb6e0c6" class="outline-4">
<h4 id="orgcb6e0c6"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div id="outline-container-org5bd1227" class="outline-4">
<h4 id="org5bd1227"><span class="section-number-4">1.1.9</span> Terminate</h4>
<div class="outline-text-4" id="text-1-1-9">
<div class="org-src-container">
<pre class="src src-f90"> <span style="color: #a020f0;">deallocate</span>( D, h0, G, W )
@ -685,7 +685,7 @@ E = E + E_nn
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-01-07 Fri 17:48</p>
<p class="date">Created: 2022-01-07 Fri 18:41</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-01-07 Fri 17:48 -->
<!-- 2022-01-07 Fri 18:41 -->
<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: 2022-01-07 Fri 17:48</p>
<p class="date">Created: 2022-01-07 Fri 18:41</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<head>
<!-- 2022-01-07 Fri 17:48 -->
<!-- 2022-01-07 Fri 18:41 -->
<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="#orgfa4098c">1. Coding conventions</a>
<li><a href="#org76fb7de">1. Coding conventions</a>
<ul>
<li><a href="#orgf665e33">1.1. Memory allocation</a></li>
<li><a href="#org31cf5d9">1.1. Memory allocation</a></li>
</ul>
</li>
<li><a href="#orgb103879">2. Front end</a>
<li><a href="#org700a3ed">2. Front end</a>
<ul>
<li><a href="#org2757fef">2.1. Error handling</a>
<li><a href="#orgd3f97d6">2.1. Error handling</a>
<ul>
<li><a href="#orgcf5614e">2.1.1. Decoding errors</a>
<li><a href="#org61f6247">2.1.1. Decoding errors</a>
<ul>
<li><a href="#org227e7ec">2.1.1.1. C source code</a></li>
<li><a href="#org16ac32a">2.1.1.2. Fortran interface</a></li>
<li><a href="#org0ee8e30">2.1.1.3. Python interface</a></li>
<li><a href="#org494e9c5">2.1.1.1. C source code</a></li>
<li><a href="#org6133135">2.1.1.2. Fortran interface</a></li>
<li><a href="#orge1aa616">2.1.1.3. Python interface</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgaac91d9">2.2. Back ends</a>
<li><a href="#orgd57618c">2.2. Back ends</a>
<ul>
<li><a href="#org29f5c04">2.2.1. C</a></li>
<li><a href="#orgd91fd32">2.2.2. Fortran</a></li>
<li><a href="#org2e875a5">2.2.3. Python</a></li>
<li><a href="#orga08a657">2.2.1. C</a></li>
<li><a href="#org28bd3f0">2.2.2. Fortran</a></li>
<li><a href="#org0093e98">2.2.3. Python</a></li>
</ul>
</li>
<li><a href="#orga41c1c9">2.3. Read/write behavior</a></li>
<li><a href="#org719625f">2.4. TREXIO file type</a>
<li><a href="#org1ec1de2">2.3. Read/write behavior</a></li>
<li><a href="#org429171a">2.4. TREXIO file type</a>
<ul>
<li><a href="#org26d9ff1">2.4.1. TREXIO<sub>File</sub> Python class</a></li>
<li><a href="#orgbb00169">2.4.1. TREXIO<sub>File</sub> Python class</a></li>
</ul>
</li>
<li><a href="#org4587422">2.5. Polymorphism of the file handle</a></li>
<li><a href="#orgd4f1681">2.6. File opening</a>
<li><a href="#org1c97f5e">2.5. Polymorphism of the file handle</a></li>
<li><a href="#orgf9b8bb6">2.6. File opening</a>
<ul>
<li><a href="#orgda9058d">2.6.1. C</a></li>
<li><a href="#org07e7786">2.6.2. Fortran</a></li>
<li><a href="#org54fdd8a">2.6.3. Python</a></li>
<li><a href="#org13e9f57">2.6.4. Zero-based versus one-based arrays of indices</a></li>
<li><a href="#orge3f0c72">2.6.1. C</a></li>
<li><a href="#orgff4dd01">2.6.2. Fortran</a></li>
<li><a href="#orga0f3ae4">2.6.3. Python</a></li>
<li><a href="#org5c7c83b">2.6.4. Zero-based versus one-based arrays of indices</a></li>
</ul>
</li>
<li><a href="#org3a329a4">2.7. File closing</a>
<li><a href="#org43bd550">2.7. File closing</a>
<ul>
<li><a href="#org0c5179c">2.7.1. C</a></li>
<li><a href="#org9255b43">2.7.2. Fortran</a></li>
<li><a href="#orgffd4606">2.7.3. Python</a></li>
<li><a href="#orge2fb150">2.7.1. C</a></li>
<li><a href="#org6dc2f0d">2.7.2. Fortran</a></li>
<li><a href="#org0c153b8">2.7.3. Python</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgc6c16b0">3. Templates for front end</a>
<li><a href="#orgf797750">3. Templates for front end</a>
<ul>
<li><a href="#orga4451bb">3.1. Description</a></li>
<li><a href="#org6cec8bb">3.2. Templates for front end has/read/write a single numerical attribute</a>
<li><a href="#org3bf8b9a">3.1. Description</a></li>
<li><a href="#org41b8d3b">3.2. Templates for front end has/read/write a single numerical attribute</a>
<ul>
<li><a href="#org873f5af">3.2.1. Introduction</a></li>
<li><a href="#orgb25e0e4">3.2.2. C templates for front end</a>
<li><a href="#orgc6518bc">3.2.1. Introduction</a></li>
<li><a href="#org616c9d0">3.2.2. C templates for front end</a>
<ul>
<li><a href="#orgff3ec9c">3.2.2.1. Function declarations</a></li>
<li><a href="#orgf92512d">3.2.2.2. Source code for double precision functions</a></li>
<li><a href="#orgb538b47">3.2.2.3. Source code for single precision functions</a></li>
<li><a href="#org926e75d">3.2.2.4. Source code for default functions</a></li>
<li><a href="#org1aa3d95">3.2.2.1. Function declarations</a></li>
<li><a href="#org3e614b3">3.2.2.2. Source code for double precision functions</a></li>
<li><a href="#org0d22f81">3.2.2.3. Source code for single precision functions</a></li>
<li><a href="#orgcdc66ce">3.2.2.4. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#org533f1d4">3.2.3. Fortran templates for front end</a></li>
<li><a href="#org95fefa5">3.2.4. Python templates for front end</a></li>
<li><a href="#orgad34a0e">3.2.3. Fortran templates for front end</a></li>
<li><a href="#org9f1300c">3.2.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#org05685ac">3.3. Templates for front end has/read/write a dataset of numerical data</a>
<li><a href="#org9e8e4c4">3.3. Templates for front end has/read/write a dataset of numerical data</a>
<ul>
<li><a href="#org3b7a815">3.3.1. Introduction</a></li>
<li><a href="#orgff955a0">3.3.2. C templates for front end</a>
<li><a href="#orgad5b82f">3.3.1. Introduction</a></li>
<li><a href="#org7deacac">3.3.2. C templates for front end</a>
<ul>
<li><a href="#orge4ae153">3.3.2.1. Function declarations</a></li>
<li><a href="#orgb8f44f9">3.3.2.2. Source code for double precision functions</a></li>
<li><a href="#orgd98f2be">3.3.2.3. Source code for single precision functions</a></li>
<li><a href="#orge7b1fe4">3.3.2.4. Source code for memory-safe functions</a></li>
<li><a href="#org0c7d396">3.3.2.5. Source code for default functions</a></li>
<li><a href="#org745b967">3.3.2.1. Function declarations</a></li>
<li><a href="#org6c24765">3.3.2.2. Source code for double precision functions</a></li>
<li><a href="#org4c4dcb8">3.3.2.3. Source code for single precision functions</a></li>
<li><a href="#org5d21e27">3.3.2.4. Source code for memory-safe functions</a></li>
<li><a href="#orgb89fd51">3.3.2.5. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#orgb0dc355">3.3.3. Fortran templates for front end</a></li>
<li><a href="#org5ae1587">3.3.4. Python templates for front end</a></li>
<li><a href="#org2f81896">3.3.3. Fortran templates for front end</a></li>
<li><a href="#orgbb40d60">3.3.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#org5dd339c">3.4. Templates for front end has/read/write a dataset of sparse data</a>
<li><a href="#org574f84f">3.4. Templates for front end has/read/write a dataset of sparse data</a>
<ul>
<li><a href="#orge037365">3.4.1. Introduction</a></li>
<li><a href="#org3318fc8">3.4.2. C templates for front end</a>
<li><a href="#org869789d">3.4.1. Introduction</a></li>
<li><a href="#orgb02bdbd">3.4.2. C templates for front end</a>
<ul>
<li><a href="#org158b1a2">3.4.2.1. Function declarations</a></li>
<li><a href="#org37a99de">3.4.2.2. Source code for default functions</a></li>
<li><a href="#org2119dac">3.4.2.1. Function declarations</a></li>
<li><a href="#org7f70e41">3.4.2.2. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#orgbec776f">3.4.3. Fortran templates for front end</a></li>
<li><a href="#org4927bb7">3.4.4. Python templates for front end</a></li>
<li><a href="#orge68776a">3.4.3. Fortran templates for front end</a></li>
<li><a href="#org44fbc8c">3.4.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#org60221d0">3.5. Templates for front end has/read/write a dataset of strings</a>
<li><a href="#org43a07de">3.5. Templates for front end has/read/write a dataset of strings</a>
<ul>
<li><a href="#orgccb6b3f">3.5.1. Introduction</a></li>
<li><a href="#org907df6b">3.5.2. C templates for front end</a>
<li><a href="#orgdb65774">3.5.1. Introduction</a></li>
<li><a href="#orgadd5205">3.5.2. C templates for front end</a>
<ul>
<li><a href="#orgf19dbe8">3.5.2.1. Function declarations</a></li>
<li><a href="#org73cec18">3.5.2.2. Source code for default functions</a></li>
<li><a href="#org3ccf91e">3.5.2.1. Function declarations</a></li>
<li><a href="#org055e0a4">3.5.2.2. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#org7aa9994">3.5.3. Fortran templates for front end</a></li>
<li><a href="#org93965d0">3.5.4. Python templates for front end</a></li>
<li><a href="#org10ddf73">3.5.3. Fortran templates for front end</a></li>
<li><a href="#orgdc02db8">3.5.4. Python templates for front end</a></li>
</ul>
</li>
<li><a href="#orgfb26385">3.6. Templates for front end has/read/write a single string attribute</a>
<li><a href="#org68d7779">3.6. Templates for front end has/read/write a single string attribute</a>
<ul>
<li><a href="#org2dda775">3.6.1. Introduction</a></li>
<li><a href="#org0c01b00">3.6.2. C templates for front end</a>
<li><a href="#orgf6a3e8c">3.6.1. Introduction</a></li>
<li><a href="#org35d439c">3.6.2. C templates for front end</a>
<ul>
<li><a href="#orgda9357f">3.6.2.1. Function declarations</a></li>
<li><a href="#orgdc40734">3.6.2.2. Source code for default functions</a></li>
<li><a href="#org444340d">3.6.2.1. Function declarations</a></li>
<li><a href="#orgb72138a">3.6.2.2. Source code for default functions</a></li>
</ul>
</li>
<li><a href="#org0fb493e">3.6.3. Fortran templates for front end</a></li>
<li><a href="#org0070a34">3.6.4. Python templates for front end</a></li>
<li><a href="#org3fa2b59">3.6.3. Fortran templates for front end</a></li>
<li><a href="#orgc81af02">3.6.4. Python templates for front end</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org19c7553">4. Fortran helper/wrapper functions</a></li>
<li><a href="#org3447dea">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-orgfa4098c" class="outline-2">
<h2 id="orgfa4098c"><span class="section-number-2">1</span> Coding conventions</h2>
<div id="outline-container-org76fb7de" class="outline-2">
<h2 id="org76fb7de"><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-orgf665e33" class="outline-3">
<h3 id="orgf665e33"><span class="section-number-3">1.1</span> Memory allocation</h3>
<div id="outline-container-org31cf5d9" class="outline-3">
<h3 id="org31cf5d9"><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-orgb103879" class="outline-2">
<h2 id="orgb103879"><span class="section-number-2">2</span> Front end</h2>
<div id="outline-container-org700a3ed" class="outline-2">
<h2 id="org700a3ed"><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-org2757fef" class="outline-3">
<h3 id="org2757fef"><span class="section-number-3">2.1</span> Error handling</h3>
<div id="outline-container-orgd3f97d6" class="outline-3">
<h3 id="orgd3f97d6"><span class="section-number-3">2.1</span> Error handling</h3>
<div class="outline-text-3" id="text-2-1">
<table id="org1b3c491" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge87a7bd" 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-orgcf5614e" class="outline-4">
<h4 id="orgcf5614e"><span class="section-number-4">2.1.1</span> Decoding errors</h4>
<div id="outline-container-org61f6247" class="outline-4">
<h4 id="org61f6247"><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-org227e7ec" class="outline-5">
<h5 id="org227e7ec"><span class="section-number-5">2.1.1.1</span> C source code</h5>
<div id="outline-container-org494e9c5" class="outline-5">
<h5 id="org494e9c5"><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-org16ac32a" class="outline-5">
<h5 id="org16ac32a"><span class="section-number-5">2.1.1.2</span> Fortran interface</h5>
<div id="outline-container-org6133135" class="outline-5">
<h5 id="org6133135"><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-org0ee8e30" class="outline-5">
<h5 id="org0ee8e30"><span class="section-number-5">2.1.1.3</span> Python interface</h5>
<div id="outline-container-orge1aa616" class="outline-5">
<h5 id="orge1aa616"><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-orgaac91d9" class="outline-3">
<h3 id="orgaac91d9"><span class="section-number-3">2.2</span> Back ends</h3>
<div id="outline-container-orgd57618c" class="outline-3">
<h3 id="orgd57618c"><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-org29f5c04" class="outline-4">
<h4 id="org29f5c04"><span class="section-number-4">2.2.1</span> C</h4>
<div id="outline-container-orga08a657" class="outline-4">
<h4 id="orga08a657"><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-orgd91fd32" class="outline-4">
<h4 id="orgd91fd32"><span class="section-number-4">2.2.2</span> Fortran</h4>
<div id="outline-container-org28bd3f0" class="outline-4">
<h4 id="org28bd3f0"><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-org2e875a5" class="outline-4">
<h4 id="org2e875a5"><span class="section-number-4">2.2.3</span> Python</h4>
<div id="outline-container-org0093e98" class="outline-4">
<h4 id="org0093e98"><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-orga41c1c9" class="outline-3">
<h3 id="orga41c1c9"><span class="section-number-3">2.3</span> Read/write behavior</h3>
<div id="outline-container-org1ec1de2" class="outline-3">
<h3 id="org1ec1de2"><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-org719625f" class="outline-3">
<h3 id="org719625f"><span class="section-number-3">2.4</span> TREXIO file type</h3>
<div id="outline-container-org429171a" class="outline-3">
<h3 id="org429171a"><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-org26d9ff1" class="outline-4">
<h4 id="org26d9ff1"><span class="section-number-4">2.4.1</span> TREXIO<sub>File</sub> Python class</h4>
<div id="outline-container-orgbb00169" class="outline-4">
<h4 id="orgbb00169"><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-org4587422" class="outline-3">
<h3 id="org4587422"><span class="section-number-3">2.5</span> Polymorphism of the file handle</h3>
<div id="outline-container-org1c97f5e" class="outline-3">
<h3 id="org1c97f5e"><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-orgd4f1681" class="outline-3">
<h3 id="orgd4f1681"><span class="section-number-3">2.6</span> File opening</h3>
<div id="outline-container-orgf9b8bb6" class="outline-3">
<h3 id="orgf9b8bb6"><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-orgda9058d" class="outline-4">
<h4 id="orgda9058d"><span class="section-number-4">2.6.1</span> C</h4>
<div id="outline-container-orge3f0c72" class="outline-4">
<h4 id="orge3f0c72"><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-org07e7786" class="outline-4">
<h4 id="org07e7786"><span class="section-number-4">2.6.2</span> Fortran</h4>
<div id="outline-container-orgff4dd01" class="outline-4">
<h4 id="orgff4dd01"><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-org54fdd8a" class="outline-4">
<h4 id="org54fdd8a"><span class="section-number-4">2.6.3</span> Python</h4>
<div id="outline-container-orga0f3ae4" class="outline-4">
<h4 id="orga0f3ae4"><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-org13e9f57" class="outline-4">
<h4 id="org13e9f57"><span class="section-number-4">2.6.4</span> Zero-based versus one-based arrays of indices</h4>
<div id="outline-container-org5c7c83b" class="outline-4">
<h4 id="org5c7c83b"><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-org3a329a4" class="outline-3">
<h3 id="org3a329a4"><span class="section-number-3">2.7</span> File closing</h3>
<div id="outline-container-org43bd550" class="outline-3">
<h3 id="org43bd550"><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-org0c5179c" class="outline-4">
<h4 id="org0c5179c"><span class="section-number-4">2.7.1</span> C</h4>
<div id="outline-container-orge2fb150" class="outline-4">
<h4 id="orge2fb150"><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-org9255b43" class="outline-4">
<h4 id="org9255b43"><span class="section-number-4">2.7.2</span> Fortran</h4>
<div id="outline-container-org6dc2f0d" class="outline-4">
<h4 id="org6dc2f0d"><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-orgffd4606" class="outline-4">
<h4 id="orgffd4606"><span class="section-number-4">2.7.3</span> Python</h4>
<div id="outline-container-org0c153b8" class="outline-4">
<h4 id="org0c153b8"><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-orgc6c16b0" class="outline-2">
<h2 id="orgc6c16b0"><span class="section-number-2">3</span> Templates for front end</h2>
<div id="outline-container-orgf797750" class="outline-2">
<h2 id="orgf797750"><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-orga4451bb" class="outline-3">
<h3 id="orga4451bb"><span class="section-number-3">3.1</span> Description</h3>
<div id="outline-container-org3bf8b9a" class="outline-3">
<h3 id="org3bf8b9a"><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-org6cec8bb" class="outline-3">
<h3 id="org6cec8bb"><span class="section-number-3">3.2</span> Templates for front end has/read/write a single numerical attribute</h3>
<div id="outline-container-org41b8d3b" class="outline-3">
<h3 id="org41b8d3b"><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-org873f5af" class="outline-4">
<h4 id="org873f5af"><span class="section-number-4">3.2.1</span> Introduction</h4>
<div id="outline-container-orgc6518bc" class="outline-4">
<h4 id="orgc6518bc"><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-orgb25e0e4" class="outline-4">
<h4 id="orgb25e0e4"><span class="section-number-4">3.2.2</span> C templates for front end</h4>
<div id="outline-container-org616c9d0" class="outline-4">
<h4 id="org616c9d0"><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-orgff3ec9c" class="outline-5">
<h5 id="orgff3ec9c"><span class="section-number-5">3.2.2.1</span> Function declarations</h5>
<div id="outline-container-org1aa3d95" class="outline-5">
<h5 id="org1aa3d95"><span class="section-number-5">3.2.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-orgf92512d" class="outline-5">
<h5 id="orgf92512d"><span class="section-number-5">3.2.2.2</span> Source code for double precision functions</h5>
<div id="outline-container-org3e614b3" class="outline-5">
<h5 id="org3e614b3"><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-orgb538b47" class="outline-5">
<h5 id="orgb538b47"><span class="section-number-5">3.2.2.3</span> Source code for single precision functions</h5>
<div id="outline-container-org0d22f81" class="outline-5">
<h5 id="org0d22f81"><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-org926e75d" class="outline-5">
<h5 id="org926e75d"><span class="section-number-5">3.2.2.4</span> Source code for default functions</h5>
<div id="outline-container-orgcdc66ce" class="outline-5">
<h5 id="orgcdc66ce"><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-org533f1d4" class="outline-4">
<h4 id="org533f1d4"><span class="section-number-4">3.2.3</span> Fortran templates for front end</h4>
<div id="outline-container-orgad34a0e" class="outline-4">
<h4 id="orgad34a0e"><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-org95fefa5" class="outline-4">
<h4 id="org95fefa5"><span class="section-number-4">3.2.4</span> Python templates for front end</h4>
<div id="outline-container-org9f1300c" class="outline-4">
<h4 id="org9f1300c"><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-org05685ac" class="outline-3">
<h3 id="org05685ac"><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-org9e8e4c4" class="outline-3">
<h3 id="org9e8e4c4"><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-org3b7a815" class="outline-4">
<h4 id="org3b7a815"><span class="section-number-4">3.3.1</span> Introduction</h4>
<div id="outline-container-orgad5b82f" class="outline-4">
<h4 id="orgad5b82f"><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-orgff955a0" class="outline-4">
<h4 id="orgff955a0"><span class="section-number-4">3.3.2</span> C templates for front end</h4>
<div id="outline-container-org7deacac" class="outline-4">
<h4 id="org7deacac"><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-orge4ae153" class="outline-5">
<h5 id="orge4ae153"><span class="section-number-5">3.3.2.1</span> Function declarations</h5>
<div id="outline-container-org745b967" class="outline-5">
<h5 id="org745b967"><span class="section-number-5">3.3.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-orgb8f44f9" class="outline-5">
<h5 id="orgb8f44f9"><span class="section-number-5">3.3.2.2</span> Source code for double precision functions</h5>
<div id="outline-container-org6c24765" class="outline-5">
<h5 id="org6c24765"><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-orgd98f2be" class="outline-5">
<h5 id="orgd98f2be"><span class="section-number-5">3.3.2.3</span> Source code for single precision functions</h5>
<div id="outline-container-org4c4dcb8" class="outline-5">
<h5 id="org4c4dcb8"><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-orge7b1fe4" class="outline-5">
<h5 id="orge7b1fe4"><span class="section-number-5">3.3.2.4</span> Source code for memory-safe functions</h5>
<div id="outline-container-org5d21e27" class="outline-5">
<h5 id="org5d21e27"><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="orgc8072ec"><span style="color: #228b22;">trexio_exit_code</span> <span style="color: #a0522d;">rc</span>;
<pre class="src src-c" id="orge42f52a"><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-org0c7d396" class="outline-5">
<h5 id="org0c7d396"><span class="section-number-5">3.3.2.5</span> Source code for default functions</h5>
<div id="outline-container-orgb89fd51" class="outline-5">
<h5 id="orgb89fd51"><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-orgb0dc355" class="outline-4">
<h4 id="orgb0dc355"><span class="section-number-4">3.3.3</span> Fortran templates for front end</h4>
<div id="outline-container-org2f81896" class="outline-4">
<h4 id="org2f81896"><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-org5ae1587" class="outline-4">
<h4 id="org5ae1587"><span class="section-number-4">3.3.4</span> Python templates for front end</h4>
<div id="outline-container-orgbb40d60" class="outline-4">
<h4 id="orgbb40d60"><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-org5dd339c" class="outline-3">
<h3 id="org5dd339c"><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-org574f84f" class="outline-3">
<h3 id="org574f84f"><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-orge037365" class="outline-4">
<h4 id="orge037365"><span class="section-number-4">3.4.1</span> Introduction</h4>
<div id="outline-container-org869789d" class="outline-4">
<h4 id="org869789d"><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-org3318fc8" class="outline-4">
<h4 id="org3318fc8"><span class="section-number-4">3.4.2</span> C templates for front end</h4>
<div id="outline-container-orgb02bdbd" class="outline-4">
<h4 id="orgb02bdbd"><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-org158b1a2" class="outline-5">
<h5 id="org158b1a2"><span class="section-number-5">3.4.2.1</span> Function declarations</h5>
<div id="outline-container-org2119dac" class="outline-5">
<h5 id="org2119dac"><span class="section-number-5">3.4.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-org37a99de" class="outline-5">
<h5 id="org37a99de"><span class="section-number-5">3.4.2.2</span> Source code for default functions</h5>
<div id="outline-container-org7f70e41" class="outline-5">
<h5 id="org7f70e41"><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-orgbec776f" class="outline-4">
<h4 id="orgbec776f"><span class="section-number-4">3.4.3</span> Fortran templates for front end</h4>
<div id="outline-container-orge68776a" class="outline-4">
<h4 id="orge68776a"><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-org4927bb7" class="outline-4">
<h4 id="org4927bb7"><span class="section-number-4">3.4.4</span> Python templates for front end</h4>
<div id="outline-container-org44fbc8c" class="outline-4">
<h4 id="org44fbc8c"><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-org60221d0" class="outline-3">
<h3 id="org60221d0"><span class="section-number-3">3.5</span> Templates for front end has/read/write a dataset of strings</h3>
<div id="outline-container-org43a07de" class="outline-3">
<h3 id="org43a07de"><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-orgccb6b3f" class="outline-4">
<h4 id="orgccb6b3f"><span class="section-number-4">3.5.1</span> Introduction</h4>
<div id="outline-container-orgdb65774" class="outline-4">
<h4 id="orgdb65774"><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-org907df6b" class="outline-4">
<h4 id="org907df6b"><span class="section-number-4">3.5.2</span> C templates for front end</h4>
<div id="outline-container-orgadd5205" class="outline-4">
<h4 id="orgadd5205"><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-orgf19dbe8" class="outline-5">
<h5 id="orgf19dbe8"><span class="section-number-5">3.5.2.1</span> Function declarations</h5>
<div id="outline-container-org3ccf91e" class="outline-5">
<h5 id="org3ccf91e"><span class="section-number-5">3.5.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-org73cec18" class="outline-5">
<h5 id="org73cec18"><span class="section-number-5">3.5.2.2</span> Source code for default functions</h5>
<div id="outline-container-org055e0a4" class="outline-5">
<h5 id="org055e0a4"><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-org7aa9994" class="outline-4">
<h4 id="org7aa9994"><span class="section-number-4">3.5.3</span> Fortran templates for front end</h4>
<div id="outline-container-org10ddf73" class="outline-4">
<h4 id="org10ddf73"><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-org93965d0" class="outline-4">
<h4 id="org93965d0"><span class="section-number-4">3.5.4</span> Python templates for front end</h4>
<div id="outline-container-orgdc02db8" class="outline-4">
<h4 id="orgdc02db8"><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-orgfb26385" class="outline-3">
<h3 id="orgfb26385"><span class="section-number-3">3.6</span> Templates for front end has/read/write a single string attribute</h3>
<div id="outline-container-org68d7779" class="outline-3">
<h3 id="org68d7779"><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-org2dda775" class="outline-4">
<h4 id="org2dda775"><span class="section-number-4">3.6.1</span> Introduction</h4>
<div id="outline-container-orgf6a3e8c" class="outline-4">
<h4 id="orgf6a3e8c"><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-org0c01b00" class="outline-4">
<h4 id="org0c01b00"><span class="section-number-4">3.6.2</span> C templates for front end</h4>
<div id="outline-container-org35d439c" class="outline-4">
<h4 id="org35d439c"><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-orgda9357f" class="outline-5">
<h5 id="orgda9357f"><span class="section-number-5">3.6.2.1</span> Function declarations</h5>
<div id="outline-container-org444340d" class="outline-5">
<h5 id="org444340d"><span class="section-number-5">3.6.2.1</span> Function declarations</h5>
</div>
<div id="outline-container-orgdc40734" class="outline-5">
<h5 id="orgdc40734"><span class="section-number-5">3.6.2.2</span> Source code for default functions</h5>
<div id="outline-container-orgb72138a" class="outline-5">
<h5 id="orgb72138a"><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-org0fb493e" class="outline-4">
<h4 id="org0fb493e"><span class="section-number-4">3.6.3</span> Fortran templates for front end</h4>
<div id="outline-container-org3fa2b59" class="outline-4">
<h4 id="org3fa2b59"><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-org0070a34" class="outline-4">
<h4 id="org0070a34"><span class="section-number-4">3.6.4</span> Python templates for front end</h4>
<div id="outline-container-orgc81af02" class="outline-4">
<h4 id="orgc81af02"><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-org19c7553" class="outline-2">
<h2 id="org19c7553"><span class="section-number-2">4</span> Fortran helper/wrapper functions</h2>
<div id="outline-container-org3447dea" class="outline-2">
<h2 id="org3447dea"><span class="section-number-2">4</span> Fortran helper/wrapper functions</h2>
<div class="outline-text-2" id="text-4">
<p>
The function below adapts the original C-based <code>trexio_open</code> for Fortran.
@ -5083,7 +5083,7 @@ two code are identical, i.e. if the <code>assert</code> statement pass.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-01-07 Fri 17:48</p>
<p class="date">Created: 2022-01-07 Fri 18:41</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

64
templator_hdf5.html
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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-01-07 Fri 17:48 -->
<!-- 2022-01-07 Fri 18:41 -->
<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="#org08d527f">1. HDF5 back end</a>
<li><a href="#org21d0d99">1. HDF5 back end</a>
<ul>
<li><a href="#org5ed3bd8">1.1. Template for HDF5 definitions</a></li>
<li><a href="#org181d4e7">1.2. Template for HDF5 structures</a></li>
<li><a href="#org1a71ccf">1.3. Template for HDF5 init/deinit</a></li>
<li><a href="#org49b7ec5">1.4. Template for HDF5 has/read/write the numerical attribute</a></li>
<li><a href="#org115b989">1.5. Template for HDF5 has/read/write the dataset of numerical data</a></li>
<li><a href="#org5b6fd6d">1.6. Template for HDF5 has/read/write the dataset of sparse data</a></li>
<li><a href="#org0432c42">1.7. Template for HDF5 has/read/write the dataset of strings</a></li>
<li><a href="#orgdf01d3e">1.8. Template for HDF5 has/read/write the string attribute</a></li>
<li><a href="#orgc2dff4e">1.9. Helper functions</a></li>
<li><a href="#orgb481285">1.1. Template for HDF5 definitions</a></li>
<li><a href="#orgbdf43c6">1.2. Template for HDF5 structures</a></li>
<li><a href="#orge33fbb5">1.3. Template for HDF5 init/deinit</a></li>
<li><a href="#org328c90e">1.4. Template for HDF5 has/read/write the numerical attribute</a></li>
<li><a href="#org25ffea7">1.5. Template for HDF5 has/read/write the dataset of numerical data</a></li>
<li><a href="#org7508fc7">1.6. Template for HDF5 has/read/write the dataset of sparse data</a></li>
<li><a href="#org6b54333">1.7. Template for HDF5 has/read/write the dataset of strings</a></li>
<li><a href="#orgc29f2b6">1.8. Template for HDF5 has/read/write the string attribute</a></li>
<li><a href="#orgae3e0bf">1.9. Helper functions</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org08d527f" class="outline-2">
<h2 id="org08d527f"><span class="section-number-2">1</span> HDF5 back end</h2>
<div id="outline-container-org21d0d99" class="outline-2">
<h2 id="org21d0d99"><span class="section-number-2">1</span> HDF5 back end</h2>
<div class="outline-text-2" id="text-1">
</div>
<div id="outline-container-org5ed3bd8" class="outline-3">
<h3 id="org5ed3bd8"><span class="section-number-3">1.1</span> Template for HDF5 definitions</h3>
<div id="outline-container-orgb481285" class="outline-3">
<h3 id="orgb481285"><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-org181d4e7" class="outline-3">
<h3 id="org181d4e7"><span class="section-number-3">1.2</span> Template for HDF5 structures</h3>
<div id="outline-container-orgbdf43c6" class="outline-3">
<h3 id="orgbdf43c6"><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-org1a71ccf" class="outline-3">
<h3 id="org1a71ccf"><span class="section-number-3">1.3</span> Template for HDF5 init/deinit</h3>
<div id="outline-container-orge33fbb5" class="outline-3">
<h3 id="orge33fbb5"><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-org49b7ec5" class="outline-3">
<h3 id="org49b7ec5"><span class="section-number-3">1.4</span> Template for HDF5 has/read/write the numerical attribute</h3>
<div id="outline-container-org328c90e" class="outline-3">
<h3 id="org328c90e"><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-org115b989" class="outline-3">
<h3 id="org115b989"><span class="section-number-3">1.5</span> Template for HDF5 has/read/write the dataset of numerical data</h3>
<div id="outline-container-org25ffea7" class="outline-3">
<h3 id="org25ffea7"><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-org5b6fd6d" class="outline-3">
<h3 id="org5b6fd6d"><span class="section-number-3">1.6</span> Template for HDF5 has/read/write the dataset of sparse data</h3>
<div id="outline-container-org7508fc7" class="outline-3">
<h3 id="org7508fc7"><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-org0432c42" class="outline-3">
<h3 id="org0432c42"><span class="section-number-3">1.7</span> Template for HDF5 has/read/write the dataset of strings</h3>
<div id="outline-container-org6b54333" class="outline-3">
<h3 id="org6b54333"><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-orgdf01d3e" class="outline-3">
<h3 id="orgdf01d3e"><span class="section-number-3">1.8</span> Template for HDF5 has/read/write the string attribute</h3>
<div id="outline-container-orgc29f2b6" class="outline-3">
<h3 id="orgc29f2b6"><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-orgc2dff4e" class="outline-3">
<h3 id="orgc2dff4e"><span class="section-number-3">1.9</span> Helper functions</h3>
<div id="outline-container-orgae3e0bf" class="outline-3">
<h3 id="orgae3e0bf"><span class="section-number-3">1.9</span> Helper functions</h3>
<div class="outline-text-3" id="text-1-9">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1452,7 +1452,7 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-01-07 Fri 17:48</p>
<p class="date">Created: 2022-01-07 Fri 18:41</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

82
templator_text.html
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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-01-07 Fri 17:48 -->
<!-- 2022-01-07 Fri 18:41 -->
<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="#org55e1004">1. TEXT back end</a>
<li><a href="#orgc0c08fc">1. TEXT back end</a>
<ul>
<li><a href="#orgcee3f26">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#org21c6472">1.2. Template for general structure in text back end</a></li>
<li><a href="#orga4f250e">1.3. Initialize function (constant part)</a></li>
<li><a href="#org0e1d740">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#org3ed3b18">1.5. Template for text read struct</a></li>
<li><a href="#org64eeb4b">1.6. Template for text flush struct</a></li>
<li><a href="#org54ffb32">1.7. Template for text free memory</a></li>
<li><a href="#org20de9c7">1.8. Template for has/read/write the numerical attribute</a></li>
<li><a href="#org9cdc251">1.9. Template for has/read/write the dataset of numerical data</a></li>
<li><a href="#org10f84d5">1.10. Template for has/read/write the dataset of strings</a></li>
<li><a href="#orga4be444">1.11. Template for has/read/write the string attribute</a></li>
<li><a href="#orgd2df7fe">1.12. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org5080f21">1.1. Template for group-related structures in text back end</a></li>
<li><a href="#orgd47f9af">1.2. Template for general structure in text back end</a></li>
<li><a href="#orged3a128">1.3. Initialize function (constant part)</a></li>
<li><a href="#org7db2fc9">1.4. Deinitialize function (templated part)</a></li>
<li><a href="#org559f5ef">1.5. Template for text read struct</a></li>
<li><a href="#org735cc8f">1.6. Template for text flush struct</a></li>
<li><a href="#orgd47018d">1.7. Template for text free memory</a></li>
<li><a href="#org48992fb">1.8. Template for has/read/write the numerical attribute</a></li>
<li><a href="#orga3daa4f">1.9. Template for has/read/write the dataset of numerical data</a></li>
<li><a href="#org941efe9">1.10. Template for has/read/write the dataset of strings</a></li>
<li><a href="#orgeb83a84">1.11. Template for has/read/write the string attribute</a></li>
<li><a href="#orgadaa5dd">1.12. Template for has/read/write the dataset of sparse data</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org55e1004" class="outline-2">
<h2 id="org55e1004"><span class="section-number-2">1</span> TEXT back end</h2>
<div id="outline-container-orgc0c08fc" class="outline-2">
<h2 id="orgc0c08fc"><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-orgcee3f26" class="outline-3">
<h3 id="orgcee3f26"><span class="section-number-3">1.1</span> Template for group-related structures in text back end</h3>
<div id="outline-container-org5080f21" class="outline-3">
<h3 id="org5080f21"><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-org21c6472" class="outline-3">
<h3 id="org21c6472"><span class="section-number-3">1.2</span> Template for general structure in text back end</h3>
<div id="outline-container-orgd47f9af" class="outline-3">
<h3 id="orgd47f9af"><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-orga4f250e" class="outline-3">
<h3 id="orga4f250e"><span class="section-number-3">1.3</span> Initialize function (constant part)</h3>
<div id="outline-container-orged3a128" class="outline-3">
<h3 id="orged3a128"><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-org0e1d740" class="outline-3">
<h3 id="org0e1d740"><span class="section-number-3">1.4</span> Deinitialize function (templated part)</h3>
<div id="outline-container-org7db2fc9" class="outline-3">
<h3 id="org7db2fc9"><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-org3ed3b18" class="outline-3">
<h3 id="org3ed3b18"><span class="section-number-3">1.5</span> Template for text read struct</h3>
<div id="outline-container-org559f5ef" class="outline-3">
<h3 id="org559f5ef"><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-org64eeb4b" class="outline-3">
<h3 id="org64eeb4b"><span class="section-number-3">1.6</span> Template for text flush struct</h3>
<div id="outline-container-org735cc8f" class="outline-3">
<h3 id="org735cc8f"><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-org54ffb32" class="outline-3">
<h3 id="org54ffb32"><span class="section-number-3">1.7</span> Template for text free memory</h3>
<div id="outline-container-orgd47018d" class="outline-3">
<h3 id="orgd47018d"><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-org20de9c7" class="outline-3">
<h3 id="org20de9c7"><span class="section-number-3">1.8</span> Template for has/read/write the numerical attribute</h3>
<div id="outline-container-org48992fb" class="outline-3">
<h3 id="org48992fb"><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-org9cdc251" class="outline-3">
<h3 id="org9cdc251"><span class="section-number-3">1.9</span> Template for has/read/write the dataset of numerical data</h3>
<div id="outline-container-orga3daa4f" class="outline-3">
<h3 id="orga3daa4f"><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-org10f84d5" class="outline-3">
<h3 id="org10f84d5"><span class="section-number-3">1.10</span> Template for has/read/write the dataset of strings</h3>
<div id="outline-container-org941efe9" class="outline-3">
<h3 id="org941efe9"><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-orga4be444" class="outline-3">
<h3 id="orga4be444"><span class="section-number-3">1.11</span> Template for has/read/write the string attribute</h3>
<div id="outline-container-orgeb83a84" class="outline-3">
<h3 id="orgeb83a84"><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-orgd2df7fe" class="outline-3">
<h3 id="orgd2df7fe"><span class="section-number-3">1.12</span> Template for has/read/write the dataset of sparse data</h3>
<div id="outline-container-orgadaa5dd" class="outline-3">
<h3 id="orgadaa5dd"><span class="section-number-3">1.12</span> Template for has/read/write the dataset of sparse data</h3>
<div class="outline-text-3" id="text-1-12">
<p>
Each sparse array is stored in a separate <code>.txt</code> file due to the fact that sparse I/O has to be decoupled
@ -1563,7 +1563,7 @@ User provides indices and values of the sparse array as two separate variables.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-01-07 Fri 17:48</p>
<p class="date">Created: 2022-01-07 Fri 18:41</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

116
trex.html
View File

@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2022-01-07 Fri 17:48 -->
<!-- 2022-01-07 Fri 18:41 -->
<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="#org91589af">1. Metadata (metadata group)</a></li>
<li><a href="#org2aa2eb6">2. Electron (electron group)</a></li>
<li><a href="#orgaa6dbba">3. Nucleus (nucleus group)</a></li>
<li><a href="#orgbcc1c34">4. Effective core potentials (ecp group)</a>
<li><a href="#org8ee7ecb">1. Metadata (metadata group)</a></li>
<li><a href="#org1032d36">2. Electron (electron group)</a></li>
<li><a href="#org44388f3">3. Nucleus (nucleus group)</a></li>
<li><a href="#org3a56e0e">4. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#orga9b5904">4.1. Example</a></li>
<li><a href="#org8536693">4.1. Example</a></li>
</ul>
</li>
<li><a href="#org84c8919">5. Basis set (basis group)</a>
<li><a href="#org862e2cd">5. Basis set (basis group)</a>
<ul>
<li><a href="#org2821632">5.1. Example</a></li>
<li><a href="#org22597b2">5.1. Example</a></li>
</ul>
</li>
<li><a href="#orgb3b386f">6. Atomic orbitals (ao group)</a>
<li><a href="#orgd15963f">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="#orgc2c9f1c">7. Molecular orbitals (mo group)</a>
<li><a href="#org00545c7">7. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org245d18b">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgc67c000">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#orge13aba9">7.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org220b8d4">7.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#org6b01b42">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#org34d35bb">9. Reduced density matrices (rdm group)</a></li>
<li><a href="#org0ed0b86">8. <span class="todo TODO">TODO</span> Slater determinants</a></li>
<li><a href="#org590d9ab">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-org91589af" class="outline-2">
<h2 id="org91589af"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org8ee7ecb" class="outline-2">
<h2 id="org8ee7ecb"><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="org504de10" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgfe625c6" 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-org2aa2eb6" class="outline-2">
<h2 id="org2aa2eb6"><span class="section-number-2">2</span> Electron (electron group)</h2>
<div id="outline-container-org1032d36" class="outline-2">
<h2 id="org1032d36"><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="org0dd5847" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf6f73a3" 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-orgaa6dbba" class="outline-2">
<h2 id="orgaa6dbba"><span class="section-number-2">3</span> Nucleus (nucleus group)</h2>
<div id="outline-container-org44388f3" class="outline-2">
<h2 id="org44388f3"><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="org88752a2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgbe239f4" 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-orgbcc1c34" class="outline-2">
<h2 id="orgbcc1c34"><span class="section-number-2">4</span> Effective core potentials (ecp group)</h2>
<div id="outline-container-org3a56e0e" class="outline-2">
<h2 id="org3a56e0e"><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="org7b25a41" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org6902d0b" 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-orga9b5904" class="outline-3">
<h3 id="orga9b5904"><span class="section-number-3">4.1</span> Example</h3>
<div id="outline-container-org8536693" class="outline-3">
<h3 id="org8536693"><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-org84c8919" class="outline-2">
<h2 id="org84c8919"><span class="section-number-2">5</span> Basis set (basis group)</h2>
<div id="outline-container-org862e2cd" class="outline-2">
<h2 id="org862e2cd"><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="orgf7916fb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge1c76ff" 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-org2821632" class="outline-3">
<h3 id="org2821632"><span class="section-number-3">5.1</span> Example</h3>
<div id="outline-container-org22597b2" class="outline-3">
<h3 id="org22597b2"><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-orgb3b386f" class="outline-2">
<h2 id="orgb3b386f"><span class="section-number-2">6</span> Atomic orbitals (ao group)</h2>
<div id="outline-container-orgd15963f" class="outline-2">
<h2 id="orgd15963f"><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="#org84c8919">Basis set</a> section) to \(\mathcal{N}_{z^2}\), which is the
the <a href="#org862e2cd">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="org1b71992" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org1b27b79" 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-orgfd47b5a" class="outline-3">
<h3 id="ao_one_e"><a id="orgfd47b5a"></a><span class="section-number-3">6.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h3>
<div id="outline-container-org41b773e" class="outline-3">
<h3 id="ao_one_e"><a id="org41b773e"></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="org0cba112" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb5d427c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1229,8 +1229,8 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org3226e27" class="outline-3">
<h3 id="ao_two_e"><a id="org3226e27"></a><span class="section-number-3">6.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h3>
<div id="outline-container-org1512c78" class="outline-3">
<h3 id="ao_two_e"><a id="org1512c78"></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="orgb7d50f4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org4ce250c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1291,10 +1291,10 @@ notation.
</div>
</div>
<div id="outline-container-orgc2c9f1c" class="outline-2">
<h2 id="orgc2c9f1c"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div id="outline-container-org00545c7" class="outline-2">
<h2 id="org00545c7"><span class="section-number-2">7</span> Molecular orbitals (mo group)</h2>
<div class="outline-text-2" id="text-7">
<table id="org4f4839d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf61f4ad" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1360,8 +1360,8 @@ notation.
</table>
</div>
<div id="outline-container-org245d18b" class="outline-3">
<h3 id="org245d18b"><span class="section-number-3">7.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h3>
<div id="outline-container-orge13aba9" class="outline-3">
<h3 id="orge13aba9"><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="org0ce07a5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd2ff988" 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-orgc67c000" class="outline-3">
<h3 id="orgc67c000"><span class="section-number-3">7.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h3>
<div id="outline-container-org220b8d4" class="outline-3">
<h3 id="org220b8d4"><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="org04b91ea" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org6639d50" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1485,13 +1485,13 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org6b01b42" class="outline-2">
<h2 id="org6b01b42"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
<div id="outline-container-org0ed0b86" class="outline-2">
<h2 id="org0ed0b86"><span class="section-number-2">8</span> <span class="todo TODO">TODO</span> Slater determinants</h2>
</div>
<div id="outline-container-org34d35bb" class="outline-2">
<h2 id="org34d35bb"><span class="section-number-2">9</span> Reduced density matrices (rdm group)</h2>
<div id="outline-container-org590d9ab" class="outline-2">
<h2 id="org590d9ab"><span class="section-number-2">9</span> Reduced density matrices (rdm group)</h2>
<div class="outline-text-2" id="text-9">
<table id="orgfb302c9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org6606c9e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1567,7 +1567,7 @@ the basis of molecular orbitals.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2022-01-07 Fri 17:48</p>
<p class="date">Created: 2022-01-07 Fri 18:41</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>