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README.html
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<head>
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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: 2023-03-26 Sun 11:56</p>
<p class="date">Created: 2023-03-28 Tue 08:43</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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examples.html
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<head>
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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="#orge06a6e8">1. Writing nuclear coordinates</a>
<li><a href="#org74e9ed7">1. Writing nuclear coordinates</a>
<ul>
<li><a href="#orgfe135ce">1.1. C</a></li>
<li><a href="#org8e1dd0f">1.2. Python</a></li>
<li><a href="#org9ba64ad">1.3. Fortran</a></li>
<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>
</ul>
</li>
<li><a href="#org9a554fa">2. Accessing sparse quantities (integrals)</a>
<li><a href="#org1c2db68">2. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#org6ed9117">2.1. Fortran</a>
<li><a href="#org21d349b">2.1. Fortran</a>
<ul>
<li><a href="#orgbe87089">2.1.1. Declare Temporary variables</a></li>
<li><a href="#orgc0e34fb">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org4e11356">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org5a2ff51">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orgd416314">2.1.5. Allocate memory</a></li>
<li><a href="#org63406c5">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org952f86f">2.1.7. Read two-electron quantities</a>
<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>
<ul>
<li><a href="#orgb7fb044">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org3f75546">2.1.7.2. Reduced density matrix</a></li>
<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>
</ul>
</li>
<li><a href="#org0b5e18a">2.1.8. Compute the energy</a></li>
<li><a href="#org1951a51">2.1.9. Terminate</a></li>
<li><a href="#org6398c39">2.1.8. Compute the energy</a></li>
<li><a href="#orgb7ac80d">2.1.9. Terminate</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgc7bd965">3. Reading determinants</a>
<li><a href="#org2d6da3e">3. Reading determinants</a>
<ul>
<li><a href="#orgc4bcd55">3.1. Fortran</a></li>
<li><a href="#org3d3a192">3.1. Fortran</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-orge06a6e8" class="outline-2">
<h2 id="orge06a6e8"><span class="section-number-2">1</span> Writing nuclear coordinates</h2>
<div id="outline-container-org74e9ed7" class="outline-2">
<h2 id="org74e9ed7"><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-orgfe135ce" class="outline-3">
<h3 id="orgfe135ce"><span class="section-number-3">1.1</span> C</h3>
<div id="outline-container-orgba14f43" class="outline-3">
<h3 id="orgba14f43"><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-org8e1dd0f" class="outline-3">
<h3 id="org8e1dd0f"><span class="section-number-3">1.2</span> Python</h3>
<div id="outline-container-orgec236d4" class="outline-3">
<h3 id="orgec236d4"><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-org9ba64ad" class="outline-3">
<h3 id="org9ba64ad"><span class="section-number-3">1.3</span> Fortran</h3>
<div id="outline-container-org64310dd" class="outline-3">
<h3 id="org64310dd"><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-org9a554fa" class="outline-2">
<h2 id="org9a554fa"><span class="section-number-2">2</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-org1c2db68" class="outline-2">
<h2 id="org1c2db68"><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-org6ed9117" class="outline-3">
<h3 id="org6ed9117"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-org21d349b" class="outline-3">
<h3 id="org21d349b"><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-orgbe87089" class="outline-4">
<h4 id="orgbe87089"><span class="section-number-4">2.1.1</span> Declare Temporary variables</h4>
<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 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-orgc0e34fb" class="outline-4">
<h4 id="orgc0e34fb"><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-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 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-org4e11356" class="outline-4">
<h4 id="org4e11356"><span class="section-number-4">2.1.3</span> Read the nuclear repulsion energy</h4>
<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 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-org5a2ff51" class="outline-4">
<h4 id="org5a2ff51"><span class="section-number-4">2.1.4</span> Read the number of molecular orbitals</h4>
<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 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-orgd416314" class="outline-4">
<h4 id="orgd416314"><span class="section-number-4">2.1.5</span> Allocate memory</h4>
<div id="outline-container-org47e5fc9" class="outline-4">
<h4 id="org47e5fc9"><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-org63406c5" class="outline-4">
<h4 id="org63406c5"><span class="section-number-4">2.1.6</span> Read one-electron quantities</h4>
<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 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-org952f86f" class="outline-4">
<h4 id="org952f86f"><span class="section-number-4">2.1.7</span> Read two-electron quantities</h4>
<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 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-orgb7fb044" class="outline-5">
<h5 id="orgb7fb044"><span class="section-number-5">2.1.7.1</span> Electron repulsion integrals</h5>
<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 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-org3f75546" class="outline-5">
<h5 id="org3f75546"><span class="section-number-5">2.1.7.2</span> Reduced density matrix</h5>
<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 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-org0b5e18a" class="outline-4">
<h4 id="org0b5e18a"><span class="section-number-4">2.1.8</span> Compute the energy</h4>
<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 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-org1951a51" class="outline-4">
<h4 id="org1951a51"><span class="section-number-4">2.1.9</span> Terminate</h4>
<div id="outline-container-orgb7ac80d" class="outline-4">
<h4 id="orgb7ac80d"><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-orgc7bd965" class="outline-2">
<h2 id="orgc7bd965"><span class="section-number-2">3</span> Reading determinants</h2>
<div id="outline-container-org2d6da3e" class="outline-2">
<h2 id="org2d6da3e"><span class="section-number-2">3</span> Reading determinants</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-orgc4bcd55" class="outline-3">
<h3 id="orgc4bcd55"><span class="section-number-3">3.1</span> Fortran</h3>
<div id="outline-container-org3d3a192" class="outline-3">
<h3 id="org3d3a192"><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: 2023-03-26 Sun 11:56</p>
<p class="date">Created: 2023-03-28 Tue 08:43</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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index.html
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2023-03-26 Sun 11:56 -->
<!-- 2023-03-28 Tue 08:43 -->
<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: 2023-03-26 Sun 11:56</p>
<p class="date">Created: 2023-03-28 Tue 08:43</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>
<!-- 2023-03-26 Sun 11:56 -->
<!-- 2023-03-28 Tue 08:43 -->
<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: 2023-03-26 Sun 11:56</p>
<p class="date">Created: 2023-03-28 Tue 08:43</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

58
lib.html
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2023-03-26 Sun 11:56 -->
<!-- 2023-03-28 Tue 08:43 -->
<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="#orgcbc0053">1. Format specification</a>
<li><a href="#org0a6785b">1. Format specification</a>
<ul>
<li><a href="#orgdf44d18">1.1. Organization of the data</a></li>
<li><a href="#org2ccb0a2">1.2. Data types</a></li>
<li><a href="#org4bebbf4">1.1. Organization of the data</a></li>
<li><a href="#org18db874">1.2. Data types</a></li>
</ul>
</li>
<li><a href="#orgebc2d8b">2. The TREXIO library</a>
<li><a href="#orgf26efab">2. The TREXIO library</a>
<ul>
<li><a href="#org960da81">2.1. The front-end</a></li>
<li><a href="#org9097857">2.2. The back-end</a></li>
<li><a href="#org92097c5">2.3. Supported languages</a></li>
<li><a href="#orgcee8493">2.4. Source code generation and documentation</a></li>
<li><a href="#org0197943">2.5. Availability</a></li>
<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>
</ul>
</li>
</ul>
@ -366,8 +366,8 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-orgcbc0053" class="outline-2">
<h2 id="orgcbc0053"><span class="section-number-2">1</span> Format specification</h2>
<div id="outline-container-org0a6785b" class="outline-2">
<h2 id="org0a6785b"><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-orgdf44d18" class="outline-3">
<h3 id="orgdf44d18"><span class="section-number-3">1.1</span> Organization of the data</h3>
<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 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-org2ccb0a2" class="outline-3">
<h3 id="org2ccb0a2"><span class="section-number-3">1.2</span> Data types</h3>
<div id="outline-container-org18db874" class="outline-3">
<h3 id="org18db874"><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-orgebc2d8b" class="outline-2">
<h2 id="orgebc2d8b"><span class="section-number-2">2</span> The TREXIO library</h2>
<div id="outline-container-orgf26efab" class="outline-2">
<h2 id="orgf26efab"><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-org960da81" class="outline-3">
<h3 id="org960da81"><span class="section-number-3">2.1</span> The front-end</h3>
<div id="outline-container-orge64af72" class="outline-3">
<h3 id="orge64af72"><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-org9097857" class="outline-3">
<h3 id="org9097857"><span class="section-number-3">2.2</span> The back-end</h3>
<div id="outline-container-org72d07bd" class="outline-3">
<h3 id="org72d07bd"><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-org92097c5" class="outline-3">
<h3 id="org92097c5"><span class="section-number-3">2.3</span> Supported languages</h3>
<div id="outline-container-org7644c41" class="outline-3">
<h3 id="org7644c41"><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-orgcee8493" class="outline-3">
<h3 id="orgcee8493"><span class="section-number-3">2.4</span> Source code generation and documentation</h3>
<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 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-org0197943" class="outline-3">
<h3 id="org0197943"><span class="section-number-3">2.5</span> Availability</h3>
<div id="outline-container-org9043340" class="outline-3">
<h3 id="org9043340"><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: 2023-03-26 Sun 11:56</p>
<p class="date">Created: 2023-03-28 Tue 08:43</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>
<!-- 2023-03-26 Sun 11:56 -->
<!-- 2023-03-28 Tue 08:43 -->
<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="#orgd346e1b">1. Template for HDF5 definitions</a></li>
<li><a href="#orgdfb40fd">2. Template for HDF5 structures</a></li>
<li><a href="#orgffa5f91">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orga5d3953">4. Template for HDF5 has a group</a></li>
<li><a href="#org4c3b44a">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orgb41c96e">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org86b7bba">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#orgb092493">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org2abcc52">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#orgc13ff2f">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org4ffde08">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#orgeb7980d">12. Source code for the determinant part</a></li>
<li><a href="#org2c2f24c">13. Helper functions</a></li>
<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>
</ul>
</div>
</div>
<div id="outline-container-orgd346e1b" class="outline-2">
<h2 id="orgd346e1b"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-org49d9f96" class="outline-2">
<h2 id="org49d9f96"><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-orgdfb40fd" class="outline-2">
<h2 id="orgdfb40fd"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-org663d63f" class="outline-2">
<h2 id="org663d63f"><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-orgffa5f91" class="outline-2">
<h2 id="orgffa5f91"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<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 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-orga5d3953" class="outline-2">
<h2 id="orga5d3953"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<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 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-org4c3b44a" class="outline-2">
<h2 id="org4c3b44a"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<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 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-orgb41c96e" class="outline-2">
<h2 id="orgb41c96e"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<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 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-org86b7bba" class="outline-2">
<h2 id="org86b7bba"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<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 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-orgb092493" class="outline-2">
<h2 id="orgb092493"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<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 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-org2abcc52" class="outline-2">
<h2 id="org2abcc52"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<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 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-orgc13ff2f" class="outline-2">
<h2 id="orgc13ff2f"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<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 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-org4ffde08" class="outline-2">
<h2 id="org4ffde08"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<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 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-orgeb7980d" class="outline-2">
<h2 id="orgeb7980d"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<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 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-org2c2f24c" class="outline-2">
<h2 id="org2c2f24c"><span class="section-number-2">13</span> Helper functions</h2>
<div id="outline-container-org1cd6fe5" class="outline-2">
<h2 id="org1cd6fe5"><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: 2023-03-26 Sun 11:56</p>
<p class="date">Created: 2023-03-28 Tue 08:43</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>
<!-- 2023-03-26 Sun 11:56 -->
<!-- 2023-03-28 Tue 08:43 -->
<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="#org5fa48f3">1. Template for group-related structures in text back end</a></li>
<li><a href="#org5f6e568">2. Template for general structure in text back end</a></li>
<li><a href="#org5a351a6">3. Initialize function (constant part)</a></li>
<li><a href="#orgbf9ab4c">4. Deinitialize function (templated part)</a></li>
<li><a href="#org12cb28f">5. Flush function (templated part)</a></li>
<li><a href="#org4b6a18a">6. Template for text read a group</a></li>
<li><a href="#orgf1fb1f6">7. Template for text has a group</a></li>
<li><a href="#org7f1db96">8. Template for text flush a group</a></li>
<li><a href="#orge22be5f">9. Template for text free memory</a></li>
<li><a href="#org357c6fd">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org83902c2">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orgb2951e7">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org6313d8c">13. Template for has/read/write a string attribute</a></li>
<li><a href="#orgb600ce8">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org5e9da21">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#orgec7a394">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#orgda128fc">17. Source code for the determinant part</a></li>
<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>
</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-org5fa48f3" class="outline-2">
<h2 id="org5fa48f3"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<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 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-org5f6e568" class="outline-2">
<h2 id="org5f6e568"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<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 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-org5a351a6" class="outline-2">
<h2 id="org5a351a6"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-org36090e5" class="outline-2">
<h2 id="org36090e5"><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-orgbf9ab4c" class="outline-2">
<h2 id="orgbf9ab4c"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-orge4997da" class="outline-2">
<h2 id="orge4997da"><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-org12cb28f" class="outline-2">
<h2 id="org12cb28f"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div id="outline-container-org4a694cd" class="outline-2">
<h2 id="org4a694cd"><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-org4b6a18a" class="outline-2">
<h2 id="org4b6a18a"><span class="section-number-2">6</span> Template for text read a group</h2>
<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 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-orgf1fb1f6" class="outline-2">
<h2 id="orgf1fb1f6"><span class="section-number-2">7</span> Template for text has a group</h2>
<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 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-org7f1db96" class="outline-2">
<h2 id="org7f1db96"><span class="section-number-2">8</span> Template for text flush a group</h2>
<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 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-orge22be5f" class="outline-2">
<h2 id="orge22be5f"><span class="section-number-2">9</span> Template for text free memory</h2>
<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 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-org357c6fd" class="outline-2">
<h2 id="org357c6fd"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<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 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-org83902c2" class="outline-2">
<h2 id="org83902c2"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<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 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-orgb2951e7" class="outline-2">
<h2 id="orgb2951e7"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<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 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-org6313d8c" class="outline-2">
<h2 id="org6313d8c"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<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 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-orgb600ce8" class="outline-2">
<h2 id="orgb600ce8"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<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 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-org5e9da21" class="outline-2">
<h2 id="org5e9da21"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<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 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-orgec7a394" class="outline-2">
<h2 id="orgec7a394"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<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 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-orgda128fc" class="outline-2">
<h2 id="orgda128fc"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<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 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: 2023-03-26 Sun 11:56</p>
<p class="date">Created: 2023-03-28 Tue 08:43</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

266
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>
<!-- 2023-03-26 Sun 11:56 -->
<!-- 2023-03-28 Tue 08:43 -->
<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="#org8c12314">1. Metadata (metadata group)</a></li>
<li><a href="#orge42966e">2. System</a>
<li><a href="#org610eddb">1. Metadata (metadata group)</a></li>
<li><a href="#org03377f8">2. System</a>
<ul>
<li><a href="#orgd4875f6">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org369ef24">2.2. Cell (cell group)</a></li>
<li><a href="#org1966111">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#orgf69244c">2.4. Electron (electron group)</a></li>
<li><a href="#org82444d9">2.5. Ground or excited states (state group)</a></li>
<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>
</ul>
</li>
<li><a href="#org41a8b8d">3. Basis functions</a>
<li><a href="#org22bf7f2">3. Basis functions</a>
<ul>
<li><a href="#org9407181">3.1. Basis set (basis group)</a>
<li><a href="#org3597b22">3.1. Basis set (basis group)</a>
<ul>
<li><a href="#org4cd1641">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#orgb659df2">3.1.2. Plane waves</a></li>
<li><a href="#org43d96df">3.1.3. Data definitions</a></li>
<li><a href="#org8a1ebdb">3.1.4. Example</a></li>
<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>
</ul>
</li>
<li><a href="#orgf07e829">3.2. Effective core potentials (ecp group)</a>
<li><a href="#orgc55dee6">3.2. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#orga9c0db4">3.2.1. Example</a></li>
<li><a href="#orga03fd45">3.2.1. Example</a></li>
</ul>
</li>
<li><a href="#org5746bdb">3.3. Numerical integration grid (grid group)</a></li>
<li><a href="#orgda02b48">3.3. Numerical integration grid (grid group)</a></li>
</ul>
</li>
<li><a href="#org6ecaf13">4. Orbitals</a>
<li><a href="#org9d78caa">4. Orbitals</a>
<ul>
<li><a href="#org98ca1b7">4.1. Atomic orbitals (ao group)</a>
<li><a href="#org0eacfd5">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="#org226bf37">4.2. Molecular orbitals (mo group)</a>
<li><a href="#org954b408">4.2. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org5ea5ee3">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org2b365a1">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<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>
</ul>
</li>
</ul>
</li>
<li><a href="#org8d80fe8">5. Multi-determinant information</a>
<li><a href="#org0506247">5. Multi-determinant information</a>
<ul>
<li><a href="#orge667954">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org739ce84">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#org1e2afb0">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org112b0ee">5.4. Reduced density matrices (rdm group)</a></li>
<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>
</ul>
</li>
<li><a href="#orgcde404f">6. Correlation factors</a>
<li><a href="#org93ef3c8">6. Correlation factors</a>
<ul>
<li><a href="#org9b2751c">6.1. Jastrow factor (jastrow group)</a>
<li><a href="#orgd46aa7c">6.1. Jastrow factor (jastrow group)</a>
<ul>
<li><a href="#org4dd9c0d">6.1.1. CHAMP</a></li>
<li><a href="#orge45e8f0">6.1.2. Mu</a></li>
<li><a href="#orgc9a764e">6.1.3. Table of values</a></li>
<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>
</ul>
</li>
</ul>
</li>
<li><a href="#org2b94634">7. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#orgf57ae60">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-org8c12314" class="outline-2">
<h2 id="org8c12314"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org610eddb" class="outline-2">
<h2 id="org610eddb"><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="org0963927" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org4fb667a" 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-orge42966e" class="outline-2">
<h2 id="orge42966e"><span class="section-number-2">2</span> System</h2>
<div id="outline-container-org03377f8" class="outline-2">
<h2 id="org03377f8"><span class="section-number-2">2</span> System</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-orgd4875f6" class="outline-3">
<h3 id="orgd4875f6"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
<div id="outline-container-orgc042ad0" class="outline-3">
<h3 id="orgc042ad0"><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="org427b2ed" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgcf21338" 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-org369ef24" class="outline-3">
<h3 id="org369ef24"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
<div id="outline-container-orge127c48" class="outline-3">
<h3 id="orge127c48"><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="org8d53bfa" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org61b5bba" 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-org1966111" class="outline-3">
<h3 id="org1966111"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<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 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="org5f7f4a1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb6d2e83" 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-orgf69244c" class="outline-3">
<h3 id="orgf69244c"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
<div id="outline-container-org36487fa" class="outline-3">
<h3 id="org36487fa"><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="org4d56c8e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org6ce2abf" 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-org82444d9" class="outline-3">
<h3 id="org82444d9"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
<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 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="org1caebba" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb8f0dd2" 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-org41a8b8d" class="outline-2">
<h2 id="org41a8b8d"><span class="section-number-2">3</span> Basis functions</h2>
<div id="outline-container-org22bf7f2" class="outline-2">
<h2 id="org22bf7f2"><span class="section-number-2">3</span> Basis functions</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org9407181" class="outline-3">
<h3 id="org9407181"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
<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 class="outline-text-3" id="text-3-1">
</div>
<div id="outline-container-org4cd1641" class="outline-4">
<h4 id="org4cd1641"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
<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 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-orgb659df2" class="outline-4">
<h4 id="orgb659df2"><span class="section-number-4">3.1.2</span> Plane waves</h4>
<div id="outline-container-org3d8bcdd" class="outline-4">
<h4 id="org3d8bcdd"><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-org43d96df" class="outline-4">
<h4 id="org43d96df"><span class="section-number-4">3.1.3</span> Data definitions</h4>
<div id="outline-container-org487dfd4" class="outline-4">
<h4 id="org487dfd4"><span class="section-number-4">3.1.3</span> Data definitions</h4>
<div class="outline-text-4" id="text-3-1-3">
<table id="org30c66d7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org18103ce" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1066,8 +1066,8 @@ plane waves.
</div>
</div>
<div id="outline-container-org8a1ebdb" class="outline-4">
<h4 id="org8a1ebdb"><span class="section-number-4">3.1.4</span> Example</h4>
<div id="outline-container-org4ac9374" class="outline-4">
<h4 id="org4ac9374"><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-orgf07e829" class="outline-3">
<h3 id="orgf07e829"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
<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 class="outline-text-3" id="text-3-2">
<p>
An effective core potential (ECP) \(V_A^{\text{ECP}}\) replacing the
@ -1154,31 +1154,33 @@ core electrons of atom \(A\) can be expressed as
\[
V_A^{\text{ECP}} =
V_{A \ell_{\max}+1} +
\sum_{\ell=0}^{\ell_{\max}} V_{A \ell}
\sum_{m=-\ell}^{\ell} | Y_{\ell m} \rangle \langle Y_{\ell m} |
\sum_{\ell=0}^{\ell_{\max}}
\delta V_{A \ell}\sum_{m=-\ell}^{\ell} | Y_{\ell m} \rangle \langle Y_{\ell m} |
\]
</p>
<p>
The first term in the equation above is sometimes attributed to the local channel,
while the remaining terms correspond to the non-local channel projections.
The first term in this equation is attributed to the local channel, while
the remaining terms correspond to non-local channel projections. \(\ell_{\max}\)
refers to the maximum angular momentum in the non-local component of the ECP.
The functions \(\delta V_{A \ell}\) and \(V_{A \ell_{\max}+1}\) are parameterized as:
</p>
<p>
All the functions \(V_{A\ell}\) are parameterized as:
\[
V_{A \ell}(\mathbf{r}) =
\begin{eqnarray}
\delta V_{A \ell}(\mathbf{r}) &=&
\sum_{q=1}^{N_{q \ell}}
\beta_{A q \ell}\, |\mathbf{r}-\mathbf{R}_{A}|^{n_{A q \ell}}\,
e^{-\alpha_{A q \ell} |\mathbf{r}-\mathbf{R}_{A}|^2 }
\].
e^{-\alpha_{A q \ell} |\mathbf{r}-\mathbf{R}_{A}|^2 } \nonumber\\
V_{A \ell_{\max}+1}(\mathbf{r}) &=& -\frac{Z_\text{eff}}{|\mathbf{r}-\mathbf{R}_{A}|}+\delta V_{A \ell_{\max}+1}(\mathbf{r})
\end{eqnarray}
<p>
where \(Z_\text{eff}\) is the effective nuclear charge of the center.
</p>
<p>
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="org9902894" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc3c8ec2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1282,8 +1284,8 @@ If you encounter the aforementioned issue, please report it to our
</p>
</div>
<div id="outline-container-orga9c0db4" class="outline-4">
<h4 id="orga9c0db4"><span class="section-number-4">3.2.1</span> Example</h4>
<div id="outline-container-orga03fd45" class="outline-4">
<h4 id="orga03fd45"><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
@ -1346,8 +1348,8 @@ power = [
</div>
</div>
<div id="outline-container-org5746bdb" class="outline-3">
<h3 id="org5746bdb"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
<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 class="outline-text-3" id="text-3-3">
<p>
In some applications, such as DFT calculations, integrals have to
@ -1362,7 +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="orgbedd617" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd64da8a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1479,12 +1481,12 @@ Feel free to submit a PR if you find missing options/functionalities.
</div>
</div>
<div id="outline-container-org6ecaf13" class="outline-2">
<h2 id="org6ecaf13"><span class="section-number-2">4</span> Orbitals</h2>
<div id="outline-container-org9d78caa" class="outline-2">
<h2 id="org9d78caa"><span class="section-number-2">4</span> Orbitals</h2>
<div class="outline-text-2" id="text-4">
</div>
<div id="outline-container-org98ca1b7" class="outline-3">
<h3 id="org98ca1b7"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
<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 class="outline-text-3" id="text-4-1">
<p>
AOs are defined as
@ -1565,7 +1567,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</p>
<table id="org3c18df2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge1a300b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1617,7 +1619,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</table>
</div>
<div id="outline-container-org811d8c9" class="outline-4">
<div id="outline-container-org225666a" 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">
@ -1635,7 +1637,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="org556e56c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org1b71443" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1730,7 +1732,7 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-orgb9da083" class="outline-4">
<div id="outline-container-orgdb95a77" 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>
@ -1756,7 +1758,7 @@ The Cholesky decomposition of the integrals can also be stored:
\]
</p>
<table id="orgb2e2c48" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5202cc9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1824,10 +1826,10 @@ The Cholesky decomposition of the integrals can also be stored:
</div>
</div>
<div id="outline-container-org226bf37" class="outline-3">
<h3 id="org226bf37"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<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 class="outline-text-3" id="text-4-2">
<table id="org0fd53df" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2a62647" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1914,8 +1916,8 @@ The Cholesky decomposition of the integrals can also be stored:
</table>
</div>
<div id="outline-container-org5ea5ee3" class="outline-4">
<h4 id="org5ea5ee3"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
<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 class="outline-text-4" id="text-4-2-1">
<p>
The operators as the same as those defined in the
@ -1923,7 +1925,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org8ec4e3e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2dfa3b2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2018,8 +2020,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org2b365a1" class="outline-4">
<h4 id="org2b365a1"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
<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 class="outline-text-4" id="text-4-2-2">
<p>
The operators are the same as those defined in the
@ -2027,7 +2029,7 @@ The operators are the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="orgdb75598" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2bb21f3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2096,12 +2098,12 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org8d80fe8" class="outline-2">
<h2 id="org8d80fe8"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div id="outline-container-org0506247" class="outline-2">
<h2 id="org0506247"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div class="outline-text-2" id="text-5">
</div>
<div id="outline-container-orge667954" class="outline-3">
<h3 id="orge667954"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
<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 class="outline-text-3" id="text-5-1">
<p>
The configuration interaction (CI) wave function \(\Psi\)
@ -2143,7 +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="org5253226" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb1ab74c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2189,8 +2191,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
</div>
</div>
<div id="outline-container-org739ce84" class="outline-3">
<h3 id="org739ce84"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
<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 class="outline-text-3" id="text-5-2">
<p>
The configuration interaction (CI) wave function \(\Psi\) can be
@ -2212,7 +2214,7 @@ matrix \(\langle D_I | \psi_J \rangle\) needed to project the CSFs in
the basis of Slater determinants.
</p>
<table id="org384c25d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5d03d3e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2258,8 +2260,8 @@ the basis of Slater determinants.
</div>
</div>
<div id="outline-container-org1e2afb0" class="outline-3">
<h3 id="org1e2afb0"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
<div id="outline-container-org4019169" class="outline-3">
<h3 id="org4019169"><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
@ -2330,7 +2332,7 @@ The order of the indices is chosen such that
<li>\(\dots\)</li>
</ul>
<table id="org09f7f98" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org1d364a5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2411,8 +2413,8 @@ The order of the indices is chosen such that
</div>
</div>
<div id="outline-container-org112b0ee" class="outline-3">
<h3 id="org112b0ee"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
<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 class="outline-text-3" id="text-5-4">
<p>
The reduced density matrices are defined in the basis of molecular
@ -2484,7 +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="org0e4a33b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org013630e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2615,12 +2617,12 @@ expressed in a basis of a one-electron function
</div>
</div>
<div id="outline-container-orgcde404f" class="outline-2">
<h2 id="orgcde404f"><span class="section-number-2">6</span> Correlation factors</h2>
<div id="outline-container-org93ef3c8" class="outline-2">
<h2 id="org93ef3c8"><span class="section-number-2">6</span> Correlation factors</h2>
<div class="outline-text-2" id="text-6">
</div>
<div id="outline-container-org9b2751c" class="outline-3">
<h3 id="org9b2751c"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
<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 class="outline-text-3" id="text-6-1">
<p>
The Jastrow factor is an $N$-electron function which multiplies the CI
@ -2645,8 +2647,8 @@ following:
</ul>
</div>
<div id="outline-container-org4dd9c0d" class="outline-4">
<h4 id="org4dd9c0d"><span class="section-number-4">6.1.1</span> CHAMP</h4>
<div id="outline-container-org63923d1" class="outline-4">
<h4 id="org63923d1"><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
@ -2747,8 +2749,8 @@ The terms \(J_{\text{ee},ij}^\infty\) and \(J_{\text{eN}}^\infty\) are shifts to
</div>
<div id="outline-container-orge45e8f0" class="outline-4">
<h4 id="orge45e8f0"><span class="section-number-4">6.1.2</span> Mu</h4>
<div id="outline-container-orgddbc20d" class="outline-4">
<h4 id="orgddbc20d"><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
@ -2845,10 +2847,10 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
</div>
</div>
<div id="outline-container-orgc9a764e" class="outline-4">
<h4 id="orgc9a764e"><span class="section-number-4">6.1.3</span> Table of values</h4>
<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 class="outline-text-4" id="text-6-1-3">
<table id="org1306391" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org087b99e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2952,8 +2954,8 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
</div>
</div>
<div id="outline-container-org2b94634" class="outline-2">
<h2 id="org2b94634"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
<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 class="outline-text-2" id="text-7">
<p>
In quantum Monte Carlo calculations, the wave function is evaluated
@ -2967,7 +2969,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
</p>
<table id="orga95b198" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge127af5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -3022,7 +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: 2023-03-26 Sun 11:56</p>
<p class="date">Created: 2023-03-28 Tue 08:43</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>