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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>
@ -383,7 +383,7 @@ The TREXIO library is licensed under the open-source 3-clause BSD license.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-03-28 Tue 08:43</p>
<p class="date">Created: 2023-04-03 Mon 19:42</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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<head>
<!-- 2023-03-28 Tue 08:43 -->
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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>
@ -346,46 +346,46 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org74e9ed7">1. Writing nuclear coordinates</a>
<li><a href="#org4659b9e">1. Writing nuclear coordinates</a>
<ul>
<li><a href="#orgba14f43">1.1. C</a></li>
<li><a href="#orgec236d4">1.2. Python</a></li>
<li><a href="#org64310dd">1.3. Fortran</a></li>
<li><a href="#org94ef258">1.1. C</a></li>
<li><a href="#org84721dc">1.2. Python</a></li>
<li><a href="#org2d72462">1.3. Fortran</a></li>
</ul>
</li>
<li><a href="#org1c2db68">2. Accessing sparse quantities (integrals)</a>
<li><a href="#org6d8a275">2. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#org21d349b">2.1. Fortran</a>
<li><a href="#orgd5dc247">2.1. Fortran</a>
<ul>
<li><a href="#org7d1ea71">2.1.1. Declare Temporary variables</a></li>
<li><a href="#org35774fd">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org3bc3272">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org5d9e9fd">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org47e5fc9">2.1.5. Allocate memory</a></li>
<li><a href="#orgab16d62">2.1.6. Read one-electron quantities</a></li>
<li><a href="#orgc01190c">2.1.7. Read two-electron quantities</a>
<li><a href="#orgcd5178b">2.1.1. Declare Temporary variables</a></li>
<li><a href="#org76ebab2">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgb4f4b8e">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org8246f0e">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orgf1a9f9d">2.1.5. Allocate memory</a></li>
<li><a href="#org02efdce">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org15ebc36">2.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org52db5a4">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org7be41a5">2.1.7.2. Reduced density matrix</a></li>
<li><a href="#orgb5d88c5">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org33be9b9">2.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org6398c39">2.1.8. Compute the energy</a></li>
<li><a href="#orgb7ac80d">2.1.9. Terminate</a></li>
<li><a href="#org53c3f03">2.1.8. Compute the energy</a></li>
<li><a href="#org022b304">2.1.9. Terminate</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org2d6da3e">3. Reading determinants</a>
<li><a href="#orgb8df5c0">3. Reading determinants</a>
<ul>
<li><a href="#org3d3a192">3.1. Fortran</a></li>
<li><a href="#org1fd96bd">3.1. Fortran</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org74e9ed7" class="outline-2">
<h2 id="org74e9ed7"><span class="section-number-2">1</span> Writing nuclear coordinates</h2>
<div id="outline-container-org4659b9e" class="outline-2">
<h2 id="org4659b9e"><span class="section-number-2">1</span> Writing nuclear coordinates</h2>
<div class="outline-text-2" id="text-1">
<p>
Here is a demonstration of how to use TREXIO to write the nuclear
@ -395,8 +395,8 @@ as well as the necessary TREXIO functions to perform these actions.
</p>
</div>
<div id="outline-container-orgba14f43" class="outline-3">
<h3 id="orgba14f43"><span class="section-number-3">1.1</span> C</h3>
<div id="outline-container-org94ef258" class="outline-3">
<h3 id="org94ef258"><span class="section-number-3">1.1</span> C</h3>
<div class="outline-text-3" id="text-1-1">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #483d8b;">#include</span> <span style="color: #8b2252;">&lt;stdio.h&gt;</span>
@ -446,8 +446,8 @@ as well as the necessary TREXIO functions to perform these actions.
</div>
</div>
<div id="outline-container-orgec236d4" class="outline-3">
<h3 id="orgec236d4"><span class="section-number-3">1.2</span> Python</h3>
<div id="outline-container-org84721dc" class="outline-3">
<h3 id="org84721dc"><span class="section-number-3">1.2</span> Python</h3>
<div class="outline-text-3" id="text-1-2">
<p>
This code uses the TREXIO Python binding to create a new TREXIO file named
@ -494,8 +494,8 @@ coordinates of the system.
</div>
</div>
<div id="outline-container-org64310dd" class="outline-3">
<h3 id="org64310dd"><span class="section-number-3">1.3</span> Fortran</h3>
<div id="outline-container-org2d72462" class="outline-3">
<h3 id="org2d72462"><span class="section-number-3">1.3</span> Fortran</h3>
<div class="outline-text-3" id="text-1-3">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">trexio_water</span>
@ -552,12 +552,12 @@ coordinates of the system.
</div>
</div>
<div id="outline-container-org1c2db68" class="outline-2">
<h2 id="org1c2db68"><span class="section-number-2">2</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-org6d8a275" class="outline-2">
<h2 id="org6d8a275"><span class="section-number-2">2</span> Accessing sparse quantities (integrals)</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org21d349b" class="outline-3">
<h3 id="org21d349b"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-orgd5dc247" class="outline-3">
<h3 id="orgd5dc247"><span class="section-number-3">2.1</span> Fortran</h3>
<div class="outline-text-3" id="text-2-1">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">print_energy</span>
@ -603,8 +603,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org7d1ea71" class="outline-4">
<h4 id="org7d1ea71"><span class="section-number-4">2.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-orgcd5178b" class="outline-4">
<h4 id="orgcd5178b"><span class="section-number-4">2.1.1</span> Declare Temporary variables</h4>
<div class="outline-text-4" id="text-2-1-1">
<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>
@ -619,8 +619,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org35774fd" class="outline-4">
<h4 id="org35774fd"><span class="section-number-4">2.1.2</span> Obtain the name of the TREXIO file from the command line, and open it for reading</h4>
<div id="outline-container-org76ebab2" class="outline-4">
<h4 id="org76ebab2"><span class="section-number-4">2.1.2</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-2-1-2">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">call</span> <span style="color: #0000ff;">getarg</span>(1, filename)
@ -636,8 +636,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-org3bc3272" class="outline-4">
<h4 id="org3bc3272"><span class="section-number-4">2.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orgb4f4b8e" class="outline-4">
<h4 id="orgb4f4b8e"><span class="section-number-4">2.1.3</span> Read the nuclear repulsion energy</h4>
<div class="outline-text-4" id="text-2-1-3">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_read_nucleus_repulsion(f, E_nn)
@ -651,8 +651,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-org5d9e9fd" class="outline-4">
<h4 id="org5d9e9fd"><span class="section-number-4">2.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org8246f0e" class="outline-4">
<h4 id="org8246f0e"><span class="section-number-4">2.1.4</span> Read the number of molecular orbitals</h4>
<div class="outline-text-4" id="text-2-1-4">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_read_mo_num(f, n)
@ -666,8 +666,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_HDF5
</div>
</div>
<div id="outline-container-org47e5fc9" class="outline-4">
<h4 id="org47e5fc9"><span class="section-number-4">2.1.5</span> Allocate memory</h4>
<div id="outline-container-orgf1a9f9d" class="outline-4">
<h4 id="orgf1a9f9d"><span class="section-number-4">2.1.5</span> Allocate memory</h4>
<div class="outline-text-4" id="text-2-1-5">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">allocate</span>( D(n,n), h0(n,n) )
@ -679,8 +679,8 @@ W(:,:,:,:) = 0.d0
</div>
</div>
<div id="outline-container-orgab16d62" class="outline-4">
<h4 id="orgab16d62"><span class="section-number-4">2.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org02efdce" class="outline-4">
<h4 id="org02efdce"><span class="section-number-4">2.1.6</span> Read one-electron quantities</h4>
<div class="outline-text-4" id="text-2-1-6">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_has_mo_1e_int_core_hamiltonian(f)
@ -712,8 +712,8 @@ rc = trexio_read_rdm_1e(f, D)
</div>
</div>
<div id="outline-container-orgc01190c" class="outline-4">
<h4 id="orgc01190c"><span class="section-number-4">2.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-org15ebc36" class="outline-4">
<h4 id="org15ebc36"><span class="section-number-4">2.1.7</span> Read two-electron quantities</h4>
<div class="outline-text-4" id="text-2-1-7">
<p>
Reading is done with OpenMP. Each thread reads its own buffer, and
@ -729,8 +729,8 @@ to be protected in the critical section when modified.
</p>
</div>
<div id="outline-container-org52db5a4" class="outline-5">
<h5 id="org52db5a4"><span class="section-number-5">2.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-orgb5d88c5" class="outline-5">
<h5 id="orgb5d88c5"><span class="section-number-5">2.1.7.1</span> Electron repulsion integrals</h5>
<div class="outline-text-5" id="text-2-1-7-1">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_has_mo_2e_int_eri(f)
@ -779,8 +779,8 @@ icount = BUFSIZE
</div>
</div>
<div id="outline-container-org7be41a5" class="outline-5">
<h5 id="org7be41a5"><span class="section-number-5">2.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org33be9b9" class="outline-5">
<h5 id="org33be9b9"><span class="section-number-5">2.1.7.2</span> Reduced density matrix</h5>
<div class="outline-text-5" id="text-2-1-7-2">
<div class="org-src-container">
<pre class="src src-f90">rc = trexio_has_rdm_2e(f)
@ -824,8 +824,8 @@ icount = bufsize
</div>
</div>
<div id="outline-container-org6398c39" class="outline-4">
<h4 id="org6398c39"><span class="section-number-4">2.1.8</span> Compute the energy</h4>
<div id="outline-container-org53c3f03" class="outline-4">
<h4 id="org53c3f03"><span class="section-number-4">2.1.8</span> Compute the energy</h4>
<div class="outline-text-4" id="text-2-1-8">
<p>
When the orbitals are real, we can use
@ -871,8 +871,8 @@ E = E + E_nn
</div>
</div>
<div id="outline-container-orgb7ac80d" class="outline-4">
<h4 id="orgb7ac80d"><span class="section-number-4">2.1.9</span> Terminate</h4>
<div id="outline-container-org022b304" class="outline-4">
<h4 id="org022b304"><span class="section-number-4">2.1.9</span> Terminate</h4>
<div class="outline-text-4" id="text-2-1-9">
<div class="org-src-container">
<pre class="src src-f90"> <span style="color: #a020f0;">deallocate</span>( D, h0, G, W )
@ -885,12 +885,12 @@ E = E + E_nn
</div>
</div>
<div id="outline-container-org2d6da3e" class="outline-2">
<h2 id="org2d6da3e"><span class="section-number-2">3</span> Reading determinants</h2>
<div id="outline-container-orgb8df5c0" class="outline-2">
<h2 id="orgb8df5c0"><span class="section-number-2">3</span> Reading determinants</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org3d3a192" class="outline-3">
<h3 id="org3d3a192"><span class="section-number-3">3.1</span> Fortran</h3>
<div id="outline-container-org1fd96bd" class="outline-3">
<h3 id="org1fd96bd"><span class="section-number-3">3.1</span> Fortran</h3>
<div class="outline-text-3" id="text-3-1">
<div class="org-src-container">
<pre class="src src-f90"><span style="color: #a020f0;">program</span> <span style="color: #0000ff;">test</span>
@ -969,7 +969,7 @@ end
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-03-28 Tue 08:43</p>
<p class="date">Created: 2023-04-03 Mon 19:42</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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index.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2023-03-28 Tue 08:43 -->
<!-- 2023-04-03 Mon 19:42 -->
<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>
@ -383,7 +383,7 @@ The TREXIO library is licensed under the open-source 3-clause BSD license.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-03-28 Tue 08:43</p>
<p class="date">Created: 2023-04-03 Mon 19:42</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

4
intro.html
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<head>
<!-- 2023-03-28 Tue 08:43 -->
<!-- 2023-04-03 Mon 19:42 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Motivation</title>
@ -384,7 +384,7 @@ still lacking, and the purpose of the TREXIO library is to fill this gap.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-03-28 Tue 08:43</p>
<p class="date">Created: 2023-04-03 Mon 19:42</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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58
lib.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2023-03-28 Tue 08:43 -->
<!-- 2023-04-03 Mon 19:42 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>The TREXIO library</title>
@ -346,19 +346,19 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org0a6785b">1. Format specification</a>
<li><a href="#org1fea9ef">1. Format specification</a>
<ul>
<li><a href="#org4bebbf4">1.1. Organization of the data</a></li>
<li><a href="#org18db874">1.2. Data types</a></li>
<li><a href="#org64c5ce6">1.1. Organization of the data</a></li>
<li><a href="#orgbb38589">1.2. Data types</a></li>
</ul>
</li>
<li><a href="#orgf26efab">2. The TREXIO library</a>
<li><a href="#orge486dbd">2. The TREXIO library</a>
<ul>
<li><a href="#orge64af72">2.1. The front-end</a></li>
<li><a href="#org72d07bd">2.2. The back-end</a></li>
<li><a href="#org7644c41">2.3. Supported languages</a></li>
<li><a href="#orgff867db">2.4. Source code generation and documentation</a></li>
<li><a href="#org9043340">2.5. Availability</a></li>
<li><a href="#org2d33f62">2.1. The front-end</a></li>
<li><a href="#org4fec3d8">2.2. The back-end</a></li>
<li><a href="#org235b769">2.3. Supported languages</a></li>
<li><a href="#org4e49631">2.4. Source code generation and documentation</a></li>
<li><a href="#org7ceffcd">2.5. Availability</a></li>
</ul>
</li>
</ul>
@ -366,8 +366,8 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-org0a6785b" class="outline-2">
<h2 id="org0a6785b"><span class="section-number-2">1</span> Format specification</h2>
<div id="outline-container-org1fea9ef" class="outline-2">
<h2 id="org1fea9ef"><span class="section-number-2">1</span> Format specification</h2>
<div class="outline-text-2" id="text-1">
</td>
<td>
@ -388,8 +388,8 @@ calculation are stored.
</p>
</div>
<div id="outline-container-org4bebbf4" class="outline-3">
<h3 id="org4bebbf4"><span class="section-number-3">1.1</span> Organization of the data</h3>
<div id="outline-container-org64c5ce6" class="outline-3">
<h3 id="org64c5ce6"><span class="section-number-3">1.1</span> Organization of the data</h3>
<div class="outline-text-3" id="text-1-1">
<p>
The data in TREXIO are organized into <b>groups</b>, each containing
@ -405,8 +405,8 @@ number of nuclei.
</div>
</div>
<div id="outline-container-org18db874" class="outline-3">
<h3 id="org18db874"><span class="section-number-3">1.2</span> Data types</h3>
<div id="outline-container-orgbb38589" class="outline-3">
<h3 id="orgbb38589"><span class="section-number-3">1.2</span> Data types</h3>
<div class="outline-text-3" id="text-1-2">
<p>
So that TREXIO can be used in any language, we use a limited number
@ -473,8 +473,8 @@ with the same name suffixed by <code>_im</code>.
</div>
</div>
<div id="outline-container-orgf26efab" class="outline-2">
<h2 id="orgf26efab"><span class="section-number-2">2</span> The TREXIO library</h2>
<div id="outline-container-orge486dbd" class="outline-2">
<h2 id="orge486dbd"><span class="section-number-2">2</span> The TREXIO library</h2>
<div class="outline-text-2" id="text-2">
</td>
<td>
@ -497,8 +497,8 @@ interface between the library and the physical storage.
</p>
</div>
<div id="outline-container-orge64af72" class="outline-3">
<h3 id="orge64af72"><span class="section-number-3">2.1</span> The front-end</h3>
<div id="outline-container-org2d33f62" class="outline-3">
<h3 id="org2d33f62"><span class="section-number-3">2.1</span> The front-end</h3>
<div class="outline-text-3" id="text-2-1">
<p>
By using the TREXIO library, users can store and extract data in a
@ -539,8 +539,8 @@ made are safe.
</div>
</div>
<div id="outline-container-org72d07bd" class="outline-3">
<h3 id="org72d07bd"><span class="section-number-3">2.2</span> The back-end</h3>
<div id="outline-container-org4fec3d8" class="outline-3">
<h3 id="org4fec3d8"><span class="section-number-3">2.2</span> The back-end</h3>
<div class="outline-text-3" id="text-2-2">
<p>
At present, TREXIO supports two back-ends: one relying only on the
@ -610,8 +610,8 @@ repositories.
</div>
</div>
<div id="outline-container-org7644c41" class="outline-3">
<h3 id="org7644c41"><span class="section-number-3">2.3</span> Supported languages</h3>
<div id="outline-container-org235b769" class="outline-3">
<h3 id="org235b769"><span class="section-number-3">2.3</span> Supported languages</h3>
<div class="outline-text-3" id="text-2-3">
<p>
One of the main benefits of using C as the interface for a library is
@ -668,8 +668,8 @@ via the Binder platform.
</div>
<div id="outline-container-orgff867db" class="outline-3">
<h3 id="orgff867db"><span class="section-number-3">2.4</span> Source code generation and documentation</h3>
<div id="outline-container-org4e49631" class="outline-3">
<h3 id="org4e49631"><span class="section-number-3">2.4</span> Source code generation and documentation</h3>
<div class="outline-text-3" id="text-2-4">
<p>
Source code generation is a valuable technique that can significantly
@ -723,8 +723,8 @@ regardless of their programming skills.
</div>
</div>
<div id="outline-container-org9043340" class="outline-3">
<h3 id="org9043340"><span class="section-number-3">2.5</span> Availability</h3>
<div id="outline-container-org7ceffcd" class="outline-3">
<h3 id="org7ceffcd"><span class="section-number-3">2.5</span> Availability</h3>
<div class="outline-text-3" id="text-2-5">
<p>
The TREXIO library is designed to be portable and easy to install
@ -754,7 +754,7 @@ are available in Ubuntu 23.04.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-03-28 Tue 08:43</p>
<p class="date">Created: 2023-04-03 Mon 19:42</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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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>
<!-- 2023-03-28 Tue 08:43 -->
<!-- 2023-04-03 Mon 19:41 -->
<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>
@ -324,25 +324,25 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org49d9f96">1. Template for HDF5 definitions</a></li>
<li><a href="#org663d63f">2. Template for HDF5 structures</a></li>
<li><a href="#org5607caf">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org66385e6">4. Template for HDF5 has a group</a></li>
<li><a href="#orge8922a4">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orgeb10b4c">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org9aa628a">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org2612727">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org3faa62d">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org523cdff">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orgb975cf1">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org9077f34">12. Source code for the determinant part</a></li>
<li><a href="#org1cd6fe5">13. Helper functions</a></li>
<li><a href="#orge9a3870">1. Template for HDF5 definitions</a></li>
<li><a href="#orgbaaf092">2. Template for HDF5 structures</a></li>
<li><a href="#org00f867d">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org759acf6">4. Template for HDF5 has a group</a></li>
<li><a href="#org316fd66">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orgb1c9a60">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org35fbbb5">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org9cdfccf">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#orgb2731ee">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org3eb6ccf">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orgbc93989">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org74a66f0">12. Source code for the determinant part</a></li>
<li><a href="#orgc3e6eaf">13. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-org49d9f96" class="outline-2">
<h2 id="org49d9f96"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-orge9a3870" class="outline-2">
<h2 id="orge9a3870"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div class="outline-text-2" id="text-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>
@ -354,8 +354,8 @@ for the JavaScript code in this tag.
</div>
</div>
<div id="outline-container-org663d63f" class="outline-2">
<h2 id="org663d63f"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-orgbaaf092" class="outline-2">
<h2 id="orgbaaf092"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div class="outline-text-2" id="text-2">
<p>
Polymorphism of the <code>trexio_t</code> type is handled by ensuring that the
@ -375,8 +375,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org5607caf" class="outline-2">
<h2 id="org5607caf"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-org00f867d" class="outline-2">
<h2 id="org00f867d"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div class="outline-text-2" id="text-3">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -496,8 +496,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org66385e6" class="outline-2">
<h2 id="org66385e6"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-org759acf6" class="outline-2">
<h2 id="org759acf6"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div class="outline-text-2" id="text-4">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -527,8 +527,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-orge8922a4" class="outline-2">
<h2 id="orge8922a4"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-org316fd66" class="outline-2">
<h2 id="org316fd66"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div class="outline-text-2" id="text-5">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -632,8 +632,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-orgeb10b4c" class="outline-2">
<h2 id="orgeb10b4c"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-orgb1c9a60" class="outline-2">
<h2 id="orgb1c9a60"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div class="outline-text-2" id="text-6">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -770,8 +770,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org9aa628a" class="outline-2">
<h2 id="org9aa628a"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-org35fbbb5" class="outline-2">
<h2 id="org35fbbb5"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div class="outline-text-2" id="text-7">
<p>
Sparse data is stored using extensible datasets of HDF5. Extensibility is required
@ -973,8 +973,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-org2612727" class="outline-2">
<h2 id="org2612727"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div id="outline-container-org9cdfccf" class="outline-2">
<h2 id="org9cdfccf"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div class="outline-text-2" id="text-8">
<p>
Chunked I/O in HDF5 for <code>buffered</code> data.
@ -1108,8 +1108,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
<div id="outline-container-org3faa62d" class="outline-2">
<h2 id="org3faa62d"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-orgb2731ee" class="outline-2">
<h2 id="orgb2731ee"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div class="outline-text-2" id="text-9">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1306,8 +1306,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
<div id="outline-container-org523cdff" class="outline-2">
<h2 id="org523cdff"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-org3eb6ccf" class="outline-2">
<h2 id="org3eb6ccf"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div class="outline-text-2" id="text-10">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1434,8 +1434,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
</div>
<div id="outline-container-orgb975cf1" class="outline-2">
<h2 id="orgb975cf1"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-orgbc93989" class="outline-2">
<h2 id="orgbc93989"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div class="outline-text-2" id="text-11">
<p>
<b><b>Note:</b></b> in early versions of the HDF5 library (v &lt; 1.10) unlinking an object was not working as expected
@ -1475,8 +1475,8 @@ Thus, any corrupted/lost file space will remain in the first file. The use of <c
</div>
</div>
<div id="outline-container-org9077f34" class="outline-2">
<h2 id="org9077f34"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div id="outline-container-org74a66f0" class="outline-2">
<h2 id="org74a66f0"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div class="outline-text-2" id="text-12">
<p>
Each array is stored in a separate HDF5 dataset due to the fact that determinant I/O has to be decoupled.
@ -1578,8 +1578,8 @@ Size specifies the number of data items (e.g. determinants) to process.
</div>
</div>
<div id="outline-container-org1cd6fe5" class="outline-2">
<h2 id="org1cd6fe5"><span class="section-number-2">13</span> Helper functions</h2>
<div id="outline-container-orgc3e6eaf" class="outline-2">
<h2 id="orgc3e6eaf"><span class="section-number-2">13</span> Helper functions</h2>
<div class="outline-text-2" id="text-13">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1842,7 +1842,7 @@ Size specifies the number of data items (e.g. determinants) to process.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-03-28 Tue 08:43</p>
<p class="date">Created: 2023-04-03 Mon 19:41</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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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>
<!-- 2023-03-28 Tue 08:43 -->
<!-- 2023-04-03 Mon 19:42 -->
<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>
@ -324,23 +324,23 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org04bbef7">1. Template for group-related structures in text back end</a></li>
<li><a href="#org4867f6a">2. Template for general structure in text back end</a></li>
<li><a href="#org36090e5">3. Initialize function (constant part)</a></li>
<li><a href="#orge4997da">4. Deinitialize function (templated part)</a></li>
<li><a href="#org4a694cd">5. Flush function (templated part)</a></li>
<li><a href="#org82b3b36">6. Template for text read a group</a></li>
<li><a href="#org05c4614">7. Template for text has a group</a></li>
<li><a href="#org2365296">8. Template for text flush a group</a></li>
<li><a href="#org466e873">9. Template for text free memory</a></li>
<li><a href="#org9ad7ba3">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org25ed44a">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org8ecc1bb">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orge7eb7f5">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org1a50553">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org79e556b">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org56996c2">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org3e1863c">17. Source code for the determinant part</a></li>
<li><a href="#orgbbb2eb7">1. Template for group-related structures in text back end</a></li>
<li><a href="#org013f514">2. Template for general structure in text back end</a></li>
<li><a href="#org01c891c">3. Initialize function (constant part)</a></li>
<li><a href="#org3bf17b5">4. Deinitialize function (templated part)</a></li>
<li><a href="#orgc1d2377">5. Flush function (templated part)</a></li>
<li><a href="#org70d48f5">6. Template for text read a group</a></li>
<li><a href="#orgfc739d3">7. Template for text has a group</a></li>
<li><a href="#orgf817a85">8. Template for text flush a group</a></li>
<li><a href="#org5e6a433">9. Template for text free memory</a></li>
<li><a href="#org5df93bf">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orgffb2c05">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orge7d762c">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org53a9e34">13. Template for has/read/write a string attribute</a></li>
<li><a href="#orgb4b65c4">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org982ca5a">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#orga97deb0">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#orgd18e130">17. Source code for the determinant part</a></li>
</ul>
</div>
</div>
@ -362,8 +362,8 @@ directory.
The file is written when closed, or when the flush function is called.
</p>
<div id="outline-container-org04bbef7" class="outline-2">
<h2 id="org04bbef7"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-orgbbb2eb7" class="outline-2">
<h2 id="orgbbb2eb7"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div class="outline-text-2" id="text-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 {
@ -382,8 +382,8 @@ The file is written when closed, or when the flush function is called.
</div>
</div>
<div id="outline-container-org4867f6a" class="outline-2">
<h2 id="org4867f6a"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-org013f514" class="outline-2">
<h2 id="org013f514"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div class="outline-text-2" id="text-2">
<p>
Polymorphism of the <code>trexio_t</code> type is handled by ensuring that the
@ -403,8 +403,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org36090e5" class="outline-2">
<h2 id="org36090e5"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-org01c891c" class="outline-2">
<h2 id="org01c891c"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div class="outline-text-2" id="text-3">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">bool</span>
@ -571,8 +571,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-orge4997da" class="outline-2">
<h2 id="orge4997da"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-org3bf17b5" class="outline-2">
<h2 id="org3bf17b5"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div class="outline-text-2" id="text-4">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -594,8 +594,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org4a694cd" class="outline-2">
<h2 id="org4a694cd"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div id="outline-container-orgc1d2377" class="outline-2">
<h2 id="orgc1d2377"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div class="outline-text-2" id="text-5">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -618,8 +618,8 @@ corresponding types for all back ends can be safely casted to
</div>
</div>
<div id="outline-container-org82b3b36" class="outline-2">
<h2 id="org82b3b36"><span class="section-number-2">6</span> Template for text read a group</h2>
<div id="outline-container-org70d48f5" class="outline-2">
<h2 id="org70d48f5"><span class="section-number-2">6</span> Template for text read a group</h2>
<div class="outline-text-2" id="text-6">
<div class="org-src-container">
<pre class="src src-c">$group$_t*
@ -845,8 +845,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org05c4614" class="outline-2">
<h2 id="org05c4614"><span class="section-number-2">7</span> Template for text has a group</h2>
<div id="outline-container-orgfc739d3" class="outline-2">
<h2 id="orgfc739d3"><span class="section-number-2">7</span> Template for text has a group</h2>
<div class="outline-text-2" id="text-7">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -886,8 +886,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org2365296" class="outline-2">
<h2 id="org2365296"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div id="outline-container-orgf817a85" class="outline-2">
<h2 id="orgf817a85"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div class="outline-text-2" id="text-8">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -951,8 +951,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org466e873" class="outline-2">
<h2 id="org466e873"><span class="section-number-2">9</span> Template for text free memory</h2>
<div id="outline-container-org5e6a433" class="outline-2">
<h2 id="org5e6a433"><span class="section-number-2">9</span> Template for text free memory</h2>
<div class="outline-text-2" id="text-9">
<p>
Memory is allocated when reading. The following function frees memory.
@ -1021,8 +1021,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-org9ad7ba3" class="outline-2">
<h2 id="org9ad7ba3"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-org5df93bf" class="outline-2">
<h2 id="org5df93bf"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div class="outline-text-2" id="text-10">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1085,8 +1085,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-org25ed44a" class="outline-2">
<h2 id="org25ed44a"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-orgffb2c05" class="outline-2">
<h2 id="orgffb2c05"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div class="outline-text-2" id="text-11">
<p>
The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1182,8 +1182,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org8ecc1bb" class="outline-2">
<h2 id="org8ecc1bb"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-orge7d762c" class="outline-2">
<h2 id="orge7d762c"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div class="outline-text-2" id="text-12">
<p>
The <code>group_dset</code> array is assumed allocated with the appropriate size.
@ -1284,8 +1284,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orge7eb7f5" class="outline-2">
<h2 id="orge7eb7f5"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-org53a9e34" class="outline-2">
<h2 id="org53a9e34"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div class="outline-text-2" id="text-13">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1359,8 +1359,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org1a50553" class="outline-2">
<h2 id="org1a50553"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-orgb4b65c4" class="outline-2">
<h2 id="orgb4b65c4"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div class="outline-text-2" id="text-14">
<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
@ -1650,8 +1650,8 @@ User provides indices and values of the sparse array as two separate variables.
</div>
</div>
<div id="outline-container-org79e556b" class="outline-2">
<h2 id="org79e556b"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div id="outline-container-org982ca5a" class="outline-2">
<h2 id="org982ca5a"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div class="outline-text-2" id="text-15">
<p>
Each array is stored in a separate <code>.txt</code> file due to the fact that buffered I/O has to be decoupled
@ -1881,8 +1881,8 @@ Size specifies the number of vector elements to be written.
</div>
</div>
</div>
<div id="outline-container-org56996c2" class="outline-2">
<h2 id="org56996c2"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-orga97deb0" class="outline-2">
<h2 id="orga97deb0"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div class="outline-text-2" id="text-16">
<div class="org-src-container">
<pre class="src src-c"><span style="color: #228b22;">trexio_exit_code</span>
@ -1910,8 +1910,8 @@ Size specifies the number of vector elements to be written.
</div>
</div>
<div id="outline-container-org3e1863c" class="outline-2">
<h2 id="org3e1863c"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div id="outline-container-orgd18e130" class="outline-2">
<h2 id="orgd18e130"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div class="outline-text-2" id="text-17">
<p>
Each array is stored in a separate <code>.txt</code> file due to the fact that determinant I/O has to be decoupled
@ -2103,7 +2103,7 @@ Size specifies the number of data items, e.g. determinants.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-03-28 Tue 08:43</p>
<p class="date">Created: 2023-04-03 Mon 19:42</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

242
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>
<!-- 2023-03-28 Tue 08:43 -->
<!-- 2023-04-03 Mon 19:42 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Data stored in TREXIO</title>
@ -346,70 +346,70 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org610eddb">1. Metadata (metadata group)</a></li>
<li><a href="#org03377f8">2. System</a>
<li><a href="#org4c3e2fa">1. Metadata (metadata group)</a></li>
<li><a href="#org618b09c">2. System</a>
<ul>
<li><a href="#orgc042ad0">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#orge127c48">2.2. Cell (cell group)</a></li>
<li><a href="#org0b4c6f2">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org36487fa">2.4. Electron (electron group)</a></li>
<li><a href="#orgd02925a">2.5. Ground or excited states (state group)</a></li>
<li><a href="#orgd4a4e7f">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org6751c60">2.2. Cell (cell group)</a></li>
<li><a href="#org0c271a2">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#orgca760a6">2.4. Electron (electron group)</a></li>
<li><a href="#orge517171">2.5. Ground or excited states (state group)</a></li>
</ul>
</li>
<li><a href="#org22bf7f2">3. Basis functions</a>
<li><a href="#orgb32a03a">3. Basis functions</a>
<ul>
<li><a href="#org3597b22">3.1. Basis set (basis group)</a>
<li><a href="#orgef8ac6e">3.1. Basis set (basis group)</a>
<ul>
<li><a href="#orgd355cc8">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#org3d8bcdd">3.1.2. Plane waves</a></li>
<li><a href="#org487dfd4">3.1.3. Data definitions</a></li>
<li><a href="#org4ac9374">3.1.4. Example</a></li>
<li><a href="#org1810a23">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#org83ba460">3.1.2. Plane waves</a></li>
<li><a href="#orgd2e4bc9">3.1.3. Data definitions</a></li>
<li><a href="#org7dd8bac">3.1.4. Example</a></li>
</ul>
</li>
<li><a href="#orgc55dee6">3.2. Effective core potentials (ecp group)</a>
<li><a href="#org23fda00">3.2. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#orga03fd45">3.2.1. Example</a></li>
<li><a href="#org25e47b0">3.2.1. Example</a></li>
</ul>
</li>
<li><a href="#orgda02b48">3.3. Numerical integration grid (grid group)</a></li>
<li><a href="#org3cd870e">3.3. Numerical integration grid (grid group)</a></li>
</ul>
</li>
<li><a href="#org9d78caa">4. Orbitals</a>
<li><a href="#org15e1ac0">4. Orbitals</a>
<ul>
<li><a href="#org0eacfd5">4.1. Atomic orbitals (ao group)</a>
<li><a href="#org7d272c0">4.1. Atomic orbitals (ao group)</a>
<ul>
<li><a href="#ao_one_e">4.1.1. One-electron integrals (<code>ao_1e_int</code> group)</a></li>
<li><a href="#ao_two_e">4.1.2. Two-electron integrals (<code>ao_2e_int</code> group)</a></li>
</ul>
</li>
<li><a href="#org954b408">4.2. Molecular orbitals (mo group)</a>
<li><a href="#orgd3cdb8c">4.2. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#orgef76bc4">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org276ad8d">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org6a2489b">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgf1cfc42">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org0506247">5. Multi-determinant information</a>
<li><a href="#org771ab98">5. Multi-determinant information</a>
<ul>
<li><a href="#org8e353b9">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org19bba83">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#org4019169">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#orgd7a0851">5.4. Reduced density matrices (rdm group)</a></li>
<li><a href="#orgb780186">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org82360c9">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#orga30ec16">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org929dd3e">5.4. Reduced density matrices (rdm group)</a></li>
</ul>
</li>
<li><a href="#org93ef3c8">6. Correlation factors</a>
<li><a href="#orga7b0cb6">6. Correlation factors</a>
<ul>
<li><a href="#orgd46aa7c">6.1. Jastrow factor (jastrow group)</a>
<li><a href="#org219a6ed">6.1. Jastrow factor (jastrow group)</a>
<ul>
<li><a href="#org63923d1">6.1.1. CHAMP</a></li>
<li><a href="#orgddbc20d">6.1.2. Mu</a></li>
<li><a href="#orgf8e281a">6.1.3. Table of values</a></li>
<li><a href="#orgcb5a1b3">6.1.1. CHAMP</a></li>
<li><a href="#org0cc9674">6.1.2. Mu</a></li>
<li><a href="#org3d20093">6.1.3. Table of values</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgf57ae60">7. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#org376c6e8">7. Quantum Monte Carlo data (qmc group)</a></li>
</ul>
</div>
</div>
@ -422,8 +422,8 @@ is reversed in the produced <code>trex.json</code> configuration file as the
library is written in C.
</p>
<div id="outline-container-org610eddb" class="outline-2">
<h2 id="org610eddb"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org4c3e2fa" class="outline-2">
<h2 id="org4c3e2fa"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div class="outline-text-2" id="text-1">
<p>
As we expect TREXIO files to be archived in open-data repositories,
@ -433,7 +433,7 @@ have participated to the creation of the file, a list of authors of
the file, and a textual description.
</p>
<table id="org4fb667a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org33306b5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -516,19 +516,19 @@ value can be manually overwritten (in unsafe mode) from <code>1</code> to <code>
</div>
</div>
<div id="outline-container-org03377f8" class="outline-2">
<h2 id="org03377f8"><span class="section-number-2">2</span> System</h2>
<div id="outline-container-org618b09c" class="outline-2">
<h2 id="org618b09c"><span class="section-number-2">2</span> System</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-orgc042ad0" class="outline-3">
<h3 id="orgc042ad0"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
<div id="outline-container-orgd4a4e7f" class="outline-3">
<h3 id="orgd4a4e7f"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
<div class="outline-text-3" id="text-2-1">
<p>
The nuclei are considered as fixed point charges. Coordinates are
given in Cartesian \((x,y,z)\) format.
</p>
<table id="orgcf21338" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5854dcd" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -595,15 +595,15 @@ given in Cartesian \((x,y,z)\) format.
</div>
</div>
<div id="outline-container-orge127c48" class="outline-3">
<h3 id="orge127c48"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
<div id="outline-container-org6751c60" class="outline-3">
<h3 id="org6751c60"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
<div class="outline-text-3" id="text-2-2">
<p>
3 Lattice vectors to define a box containing the system, for example
used in periodic calculations.
</p>
<table id="org61b5bba" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org6202674" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -677,15 +677,15 @@ used in periodic calculations.
</div>
</div>
<div id="outline-container-org0b4c6f2" class="outline-3">
<h3 id="org0b4c6f2"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div id="outline-container-org0c271a2" class="outline-3">
<h3 id="org0c271a2"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div class="outline-text-3" id="text-2-3">
<p>
A single $k$-point per TREXIO file can be stored. The $k$-point is
defined in this group.
</p>
<table id="orgb6d2e83" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge97d041" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -724,8 +724,8 @@ defined in this group.
</div>
</div>
<div id="outline-container-org36487fa" class="outline-3">
<h3 id="org36487fa"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
<div id="outline-container-orgca760a6" class="outline-3">
<h3 id="orgca760a6"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
<div class="outline-text-3" id="text-2-4">
<p>
The chemical system consists of nuclei and electrons, where the
@ -744,7 +744,7 @@ the number of &uarr; and &darr; electrons is fixed.
</p>
<table id="org6ce2abf" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org440562c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -790,8 +790,8 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-orgd02925a" class="outline-3">
<h3 id="orgd02925a"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
<div id="outline-container-orge517171" class="outline-3">
<h3 id="orge517171"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
<div class="outline-text-3" id="text-2-5">
<p>
This group contains information about excited states. Since only a
@ -808,7 +808,7 @@ integrals, etc.
The <code>id</code> and <code>current_label</code> attributes need to be specified for each file.
</p>
<table id="orgb8f0dd2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org4adcb69" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -869,16 +869,16 @@ The <code>id</code> and <code>current_label</code> attributes need to be specifi
</div>
</div>
<div id="outline-container-org22bf7f2" class="outline-2">
<h2 id="org22bf7f2"><span class="section-number-2">3</span> Basis functions</h2>
<div id="outline-container-orgb32a03a" class="outline-2">
<h2 id="orgb32a03a"><span class="section-number-2">3</span> Basis functions</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org3597b22" class="outline-3">
<h3 id="org3597b22"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
<div id="outline-container-orgef8ac6e" class="outline-3">
<h3 id="orgef8ac6e"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
<div class="outline-text-3" id="text-3-1">
</div>
<div id="outline-container-orgd355cc8" class="outline-4">
<h4 id="orgd355cc8"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
<div id="outline-container-org1810a23" class="outline-4">
<h4 id="org1810a23"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
<div class="outline-text-4" id="text-3-1-1">
<p>
We consider here basis functions centered on nuclei. Hence, it is
@ -932,8 +932,8 @@ All the basis set parameters are stored in one-dimensional arrays.
</div>
</div>
<div id="outline-container-org3d8bcdd" class="outline-4">
<h4 id="org3d8bcdd"><span class="section-number-4">3.1.2</span> Plane waves</h4>
<div id="outline-container-org83ba460" class="outline-4">
<h4 id="org83ba460"><span class="section-number-4">3.1.2</span> Plane waves</h4>
<div class="outline-text-4" id="text-3-1-2">
<p>
A plane wave is defined as
@ -954,10 +954,10 @@ plane waves.
</div>
</div>
<div id="outline-container-org487dfd4" class="outline-4">
<h4 id="org487dfd4"><span class="section-number-4">3.1.3</span> Data definitions</h4>
<div id="outline-container-orgd2e4bc9" class="outline-4">
<h4 id="orgd2e4bc9"><span class="section-number-4">3.1.3</span> Data definitions</h4>
<div class="outline-text-4" id="text-3-1-3">
<table id="org18103ce" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc3835df" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1066,8 +1066,8 @@ plane waves.
</div>
</div>
<div id="outline-container-org4ac9374" class="outline-4">
<h4 id="org4ac9374"><span class="section-number-4">3.1.4</span> Example</h4>
<div id="outline-container-org7dd8bac" class="outline-4">
<h4 id="org7dd8bac"><span class="section-number-4">3.1.4</span> Example</h4>
<div class="outline-text-4" id="text-3-1-4">
<p>
For example, consider H<sub>2</sub> with the following basis set (in GAMESS
@ -1145,8 +1145,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-orgc55dee6" class="outline-3">
<h3 id="orgc55dee6"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
<div id="outline-container-org23fda00" class="outline-3">
<h3 id="org23fda00"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
<div class="outline-text-3" id="text-3-2">
<p>
An effective core potential (ECP) \(V_A^{\text{ECP}}\) replacing the
@ -1180,7 +1180,7 @@ where \(Z_\text{eff}\) is the effective nuclear charge of the center.
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="orgc3c8ec2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5b8371e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1284,8 +1284,8 @@ If you encounter the aforementioned issue, please report it to our
</p>
</div>
<div id="outline-container-orga03fd45" class="outline-4">
<h4 id="orga03fd45"><span class="section-number-4">3.2.1</span> Example</h4>
<div id="outline-container-org25e47b0" class="outline-4">
<h4 id="org25e47b0"><span class="section-number-4">3.2.1</span> Example</h4>
<div class="outline-text-4" id="text-3-2-1">
<p>
For example, consider H<sub>2</sub> molecule with the following
@ -1348,8 +1348,8 @@ power = [
</div>
</div>
<div id="outline-container-orgda02b48" class="outline-3">
<h3 id="orgda02b48"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
<div id="outline-container-org3cd870e" class="outline-3">
<h3 id="org3cd870e"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
<div class="outline-text-3" id="text-3-3">
<p>
In some applications, such as DFT calculations, integrals have to
@ -1364,7 +1364,7 @@ The structure of this group is adapted for the <a href="https://github.com/dftli
Feel free to submit a PR if you find missing options/functionalities.
</p>
<table id="orgd64da8a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org8c244ba" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1481,12 +1481,12 @@ Feel free to submit a PR if you find missing options/functionalities.
</div>
</div>
<div id="outline-container-org9d78caa" class="outline-2">
<h2 id="org9d78caa"><span class="section-number-2">4</span> Orbitals</h2>
<div id="outline-container-org15e1ac0" class="outline-2">
<h2 id="org15e1ac0"><span class="section-number-2">4</span> Orbitals</h2>
<div class="outline-text-2" id="text-4">
</div>
<div id="outline-container-org0eacfd5" class="outline-3">
<h3 id="org0eacfd5"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
<div id="outline-container-org7d272c0" class="outline-3">
<h3 id="org7d272c0"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
<div class="outline-text-3" id="text-4-1">
<p>
AOs are defined as
@ -1567,7 +1567,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</p>
<table id="orge1a300b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgce7df71" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1619,7 +1619,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</table>
</div>
<div id="outline-container-org225666a" class="outline-4">
<div id="outline-container-orge4631b3" class="outline-4">
<h4 id="ao_one_e"><span class="section-number-4">4.1.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h4>
<div class="outline-text-4" id="text-ao_one_e">
<ul class="org-ul">
@ -1637,7 +1637,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="org1b71443" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org9ce2cf1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1732,7 +1732,7 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-orgdb95a77" class="outline-4">
<div id="outline-container-org8bceae8" class="outline-4">
<h4 id="ao_two_e"><span class="section-number-4">4.1.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h4>
<div class="outline-text-4" id="text-ao_two_e">
<p>
@ -1758,7 +1758,7 @@ The Cholesky decomposition of the integrals can also be stored:
\]
</p>
<table id="org5202cc9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org90833f7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1826,10 +1826,10 @@ The Cholesky decomposition of the integrals can also be stored:
</div>
</div>
<div id="outline-container-org954b408" class="outline-3">
<h3 id="org954b408"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div id="outline-container-orgd3cdb8c" class="outline-3">
<h3 id="orgd3cdb8c"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div class="outline-text-3" id="text-4-2">
<table id="org2a62647" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgabaa401" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1916,8 +1916,8 @@ The Cholesky decomposition of the integrals can also be stored:
</table>
</div>
<div id="outline-container-orgef76bc4" class="outline-4">
<h4 id="orgef76bc4"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
<div id="outline-container-org6a2489b" class="outline-4">
<h4 id="org6a2489b"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
<div class="outline-text-4" id="text-4-2-1">
<p>
The operators as the same as those defined in the
@ -1925,7 +1925,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org2dfa3b2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org4b46386" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2020,8 +2020,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org276ad8d" class="outline-4">
<h4 id="org276ad8d"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
<div id="outline-container-orgf1cfc42" class="outline-4">
<h4 id="orgf1cfc42"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
<div class="outline-text-4" id="text-4-2-2">
<p>
The operators are the same as those defined in the
@ -2029,7 +2029,7 @@ The operators are the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org2bb21f3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org8497b20" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2098,12 +2098,12 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org0506247" class="outline-2">
<h2 id="org0506247"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div id="outline-container-org771ab98" class="outline-2">
<h2 id="org771ab98"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div class="outline-text-2" id="text-5">
</div>
<div id="outline-container-org8e353b9" class="outline-3">
<h3 id="org8e353b9"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
<div id="outline-container-orgb780186" class="outline-3">
<h3 id="orgb780186"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
<div class="outline-text-3" id="text-5-1">
<p>
The configuration interaction (CI) wave function \(\Psi\)
@ -2145,7 +2145,7 @@ produced by the code generator.
An illustration on how to read determinants is presented in the <a href="./examples.html">examples</a>.
</p>
<table id="orgb1ab74c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgaecb9ec" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2191,8 +2191,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
</div>
</div>
<div id="outline-container-org19bba83" class="outline-3">
<h3 id="org19bba83"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
<div id="outline-container-org82360c9" class="outline-3">
<h3 id="org82360c9"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
<div class="outline-text-3" id="text-5-2">
<p>
The configuration interaction (CI) wave function \(\Psi\) can be
@ -2214,7 +2214,7 @@ matrix \(\langle D_I | \psi_J \rangle\) needed to project the CSFs in
the basis of Slater determinants.
</p>
<table id="org5d03d3e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org8fc74db" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2260,8 +2260,8 @@ the basis of Slater determinants.
</div>
</div>
<div id="outline-container-org4019169" class="outline-3">
<h3 id="org4019169"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
<div id="outline-container-orga30ec16" class="outline-3">
<h3 id="orga30ec16"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
<div class="outline-text-3" id="text-5-3">
<p>
The wave function may be expressed in terms of action of the cluster
@ -2332,7 +2332,7 @@ The order of the indices is chosen such that
<li>\(\dots\)</li>
</ul>
<table id="org1d364a5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org3008571" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2413,8 +2413,8 @@ The order of the indices is chosen such that
</div>
</div>
<div id="outline-container-orgd7a0851" class="outline-3">
<h3 id="orgd7a0851"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
<div id="outline-container-org929dd3e" class="outline-3">
<h3 id="org929dd3e"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
<div class="outline-text-3" id="text-5-4">
<p>
The reduced density matrices are defined in the basis of molecular
@ -2486,7 +2486,7 @@ expressed in a basis of a one-electron function
\(g_{ik}(\mathbf{r}_1) = \phi_i(\mathbf{r}_1) \phi_k(\mathbf{r}_1)\).
</p>
<table id="org013630e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org528dc78" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2617,12 +2617,12 @@ expressed in a basis of a one-electron function
</div>
</div>
<div id="outline-container-org93ef3c8" class="outline-2">
<h2 id="org93ef3c8"><span class="section-number-2">6</span> Correlation factors</h2>
<div id="outline-container-orga7b0cb6" class="outline-2">
<h2 id="orga7b0cb6"><span class="section-number-2">6</span> Correlation factors</h2>
<div class="outline-text-2" id="text-6">
</div>
<div id="outline-container-orgd46aa7c" class="outline-3">
<h3 id="orgd46aa7c"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
<div id="outline-container-org219a6ed" class="outline-3">
<h3 id="org219a6ed"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
<div class="outline-text-3" id="text-6-1">
<p>
The Jastrow factor is an $N$-electron function which multiplies the CI
@ -2647,8 +2647,8 @@ following:
</ul>
</div>
<div id="outline-container-org63923d1" class="outline-4">
<h4 id="org63923d1"><span class="section-number-4">6.1.1</span> CHAMP</h4>
<div id="outline-container-orgcb5a1b3" class="outline-4">
<h4 id="orgcb5a1b3"><span class="section-number-4">6.1.1</span> CHAMP</h4>
<div class="outline-text-4" id="text-6-1-1">
<p>
The first form of Jastrow factor is the one used in
@ -2749,8 +2749,8 @@ The terms \(J_{\text{ee},ij}^\infty\) and \(J_{\text{eN}}^\infty\) are shifts to
</div>
<div id="outline-container-orgddbc20d" class="outline-4">
<h4 id="orgddbc20d"><span class="section-number-4">6.1.2</span> Mu</h4>
<div id="outline-container-org0cc9674" class="outline-4">
<h4 id="org0cc9674"><span class="section-number-4">6.1.2</span> Mu</h4>
<div class="outline-text-4" id="text-6-1-2">
<p>
<a href="https://aip.scitation.org/doi/10.1063/5.0044683">Mu-Jastrow</a> is based on a one-parameter correlation factor that has
@ -2847,10 +2847,10 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
</div>
</div>
<div id="outline-container-orgf8e281a" class="outline-4">
<h4 id="orgf8e281a"><span class="section-number-4">6.1.3</span> Table of values</h4>
<div id="outline-container-org3d20093" class="outline-4">
<h4 id="org3d20093"><span class="section-number-4">6.1.3</span> Table of values</h4>
<div class="outline-text-4" id="text-6-1-3">
<table id="org087b99e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge012e52" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2954,8 +2954,8 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
</div>
</div>
<div id="outline-container-orgf57ae60" class="outline-2">
<h2 id="orgf57ae60"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
<div id="outline-container-org376c6e8" class="outline-2">
<h2 id="org376c6e8"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
<div class="outline-text-2" id="text-7">
<p>
In quantum Monte Carlo calculations, the wave function is evaluated
@ -2969,7 +2969,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
</p>
<table id="orge127af5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc492b66" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -3024,7 +3024,7 @@ of $&uarr;$-spin and then all the $&darr;$-spin.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-03-28 Tue 08:43</p>
<p class="date">Created: 2023-04-03 Mon 19:42</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>