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README.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2023-12-13 Wed 10:07 -->
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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>
@ -406,7 +406,7 @@ 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: 2023-12-13 Wed 10:07</p>
<p class="date">Created: 2024-01-11 Thu 15:02</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2023-12-13 Wed 10:07 -->
<!-- 2024-01-11 Thu 15:02 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Examples</title>
@ -346,61 +346,61 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgd06b503">1. Writing nuclear coordinates</a>
<li><a href="#org998cda4">1. Writing nuclear coordinates</a>
<ul>
<li><a href="#org6bd2d45">1.1. C</a></li>
<li><a href="#orgd1d51d4">1.2. Python</a></li>
<li><a href="#org79a0043">1.3. Fortran</a></li>
<li><a href="#orga2ede0f">1.1. C</a></li>
<li><a href="#org0432ce6">1.2. Python</a></li>
<li><a href="#org033ab18">1.3. Fortran</a></li>
</ul>
</li>
<li><a href="#org01d2ba2">2. Accessing sparse quantities (integrals)</a>
<li><a href="#org9c5eb11">2. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#org8060fe5">2.1. Fortran</a>
<li><a href="#org66392cf">2.1. Fortran</a>
<ul>
<li><a href="#orgc5d35b5">2.1.1. Declare Temporary variables</a></li>
<li><a href="#orgdd0ba66">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgbdac18c">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org215b140">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org074256a">2.1.5. Allocate memory</a></li>
<li><a href="#orgd736f9f">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org8244296">2.1.7. Read two-electron quantities</a>
<li><a href="#org07b1b5a">2.1.1. Declare Temporary variables</a></li>
<li><a href="#org0c1fbe3">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgf0ecb82">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org82b04b8">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org5753124">2.1.5. Allocate memory</a></li>
<li><a href="#org34a58ca">2.1.6. Read one-electron quantities</a></li>
<li><a href="#orgc9e57ae">2.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#orgaded53f">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#orgcadc83a">2.1.7.2. Reduced density matrix</a></li>
<li><a href="#orgd45fc1d">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#orgbe270e0">2.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org8992291">2.1.8. Compute the energy</a></li>
<li><a href="#orgd9e634a">2.1.9. Terminate</a></li>
<li><a href="#org3529617">2.1.8. Compute the energy</a></li>
<li><a href="#org6064bd2">2.1.9. Terminate</a></li>
</ul>
</li>
<li><a href="#org5f3a0ae">2.2. Python</a>
<li><a href="#org23166d3">2.2. Python</a>
<ul>
<li><a href="#org465bdd8">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org09232c2">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#org6356182">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#orgcf7575b">2.2.4. Read one-electron quantities</a></li>
<li><a href="#orge4cf3ec">2.2.5. Read two-electron quantities</a>
<li><a href="#orgbef5b1f">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgfe0eb3d">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#org3a3c6da">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#org21c880d">2.2.4. Read one-electron quantities</a></li>
<li><a href="#orgb70a042">2.2.5. Read two-electron quantities</a>
<ul>
<li><a href="#org8903f8c">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#org8b30e36">2.2.5.2. Reduced density matrix</a></li>
<li><a href="#org1c6c12a">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#org1ca360f">2.2.5.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org85b6c2f">2.2.6. Compute the energy</a></li>
<li><a href="#orgd0b7298">2.2.6. Compute the energy</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orge257625">3. Reading determinants</a>
<li><a href="#org20dedfe">3. Reading determinants</a>
<ul>
<li><a href="#org336aefc">3.1. Fortran</a></li>
<li><a href="#org3ff3b43">3.1. Fortran</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-orgd06b503" class="outline-2">
<h2 id="orgd06b503"><span class="section-number-2">1</span> Writing nuclear coordinates</h2>
<div id="outline-container-org998cda4" class="outline-2">
<h2 id="org998cda4"><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
@ -410,8 +410,8 @@ as well as the necessary TREXIO functions to perform these actions.
</p>
</div>
<div id="outline-container-org6bd2d45" class="outline-3">
<h3 id="org6bd2d45"><span class="section-number-3">1.1</span> C</h3>
<div id="outline-container-orga2ede0f" class="outline-3">
<h3 id="orga2ede0f"><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>
@ -461,8 +461,8 @@ as well as the necessary TREXIO functions to perform these actions.
</div>
</div>
<div id="outline-container-orgd1d51d4" class="outline-3">
<h3 id="orgd1d51d4"><span class="section-number-3">1.2</span> Python</h3>
<div id="outline-container-org0432ce6" class="outline-3">
<h3 id="org0432ce6"><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
@ -509,8 +509,8 @@ coordinates of the system.
</div>
</div>
<div id="outline-container-org79a0043" class="outline-3">
<h3 id="org79a0043"><span class="section-number-3">1.3</span> Fortran</h3>
<div id="outline-container-org033ab18" class="outline-3">
<h3 id="org033ab18"><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>
@ -567,12 +567,12 @@ coordinates of the system.
</div>
</div>
<div id="outline-container-org01d2ba2" class="outline-2">
<h2 id="org01d2ba2"><span class="section-number-2">2</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-org9c5eb11" class="outline-2">
<h2 id="org9c5eb11"><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-org8060fe5" class="outline-3">
<h3 id="org8060fe5"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-org66392cf" class="outline-3">
<h3 id="org66392cf"><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>
@ -618,8 +618,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-orgc5d35b5" class="outline-4">
<h4 id="orgc5d35b5"><span class="section-number-4">2.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org07b1b5a" class="outline-4">
<h4 id="org07b1b5a"><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>
@ -634,8 +634,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-orgdd0ba66" class="outline-4">
<h4 id="orgdd0ba66"><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-org0c1fbe3" class="outline-4">
<h4 id="org0c1fbe3"><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)
@ -651,8 +651,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_AUTO
</div>
</div>
<div id="outline-container-orgbdac18c" class="outline-4">
<h4 id="orgbdac18c"><span class="section-number-4">2.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orgf0ecb82" class="outline-4">
<h4 id="orgf0ecb82"><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)
@ -666,8 +666,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_AUTO
</div>
</div>
<div id="outline-container-org215b140" class="outline-4">
<h4 id="org215b140"><span class="section-number-4">2.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org82b04b8" class="outline-4">
<h4 id="org82b04b8"><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)
@ -681,8 +681,8 @@ f = trexio_open (filename, <span style="color: #8b2252;">'r'</span>, TREXIO_AUTO
</div>
</div>
<div id="outline-container-org074256a" class="outline-4">
<h4 id="org074256a"><span class="section-number-4">2.1.5</span> Allocate memory</h4>
<div id="outline-container-org5753124" class="outline-4">
<h4 id="org5753124"><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) )
@ -694,8 +694,8 @@ W(:,:,:,:) = 0.d0
</div>
</div>
<div id="outline-container-orgd736f9f" class="outline-4">
<h4 id="orgd736f9f"><span class="section-number-4">2.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org34a58ca" class="outline-4">
<h4 id="org34a58ca"><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)
@ -727,8 +727,8 @@ rc = trexio_read_rdm_1e(f, D)
</div>
</div>
<div id="outline-container-org8244296" class="outline-4">
<h4 id="org8244296"><span class="section-number-4">2.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-orgc9e57ae" class="outline-4">
<h4 id="orgc9e57ae"><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
@ -744,8 +744,8 @@ to be protected in the critical section when modified.
</p>
</div>
<div id="outline-container-orgaded53f" class="outline-5">
<h5 id="orgaded53f"><span class="section-number-5">2.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-orgd45fc1d" class="outline-5">
<h5 id="orgd45fc1d"><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)
@ -794,8 +794,8 @@ icount = BUFSIZE
</div>
</div>
<div id="outline-container-orgcadc83a" class="outline-5">
<h5 id="orgcadc83a"><span class="section-number-5">2.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-orgbe270e0" class="outline-5">
<h5 id="orgbe270e0"><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)
@ -839,8 +839,8 @@ icount = bufsize
</div>
</div>
<div id="outline-container-org8992291" class="outline-4">
<h4 id="org8992291"><span class="section-number-4">2.1.8</span> Compute the energy</h4>
<div id="outline-container-org3529617" class="outline-4">
<h4 id="org3529617"><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
@ -886,8 +886,8 @@ E = E + E_nn
</div>
</div>
<div id="outline-container-orgd9e634a" class="outline-4">
<h4 id="orgd9e634a"><span class="section-number-4">2.1.9</span> Terminate</h4>
<div id="outline-container-org6064bd2" class="outline-4">
<h4 id="org6064bd2"><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 )
@ -899,8 +899,8 @@ E = E + E_nn
</div>
</div>
<div id="outline-container-org5f3a0ae" class="outline-3">
<h3 id="org5f3a0ae"><span class="section-number-3">2.2</span> Python</h3>
<div id="outline-container-org23166d3" class="outline-3">
<h3 id="org23166d3"><span class="section-number-3">2.2</span> Python</h3>
<div class="outline-text-3" id="text-2-2">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">import</span> sys
@ -934,8 +934,8 @@ One needs to read from the TREXIO file:
</dl>
</div>
<div id="outline-container-org465bdd8" class="outline-4">
<h4 id="org465bdd8"><span class="section-number-4">2.2.1</span> Obtain the name of the TREXIO file from the command line, and open it for reading</h4>
<div id="outline-container-orgbef5b1f" class="outline-4">
<h4 id="orgbef5b1f"><span class="section-number-4">2.2.1</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-2-2-1">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a0522d;">filename</span> = sys.argv[1]
@ -945,8 +945,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org09232c2" class="outline-4">
<h4 id="org09232c2"><span class="section-number-4">2.2.2</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orgfe0eb3d" class="outline-4">
<h4 id="orgfe0eb3d"><span class="section-number-4">2.2.2</span> Read the nuclear repulsion energy</h4>
<div class="outline-text-4" id="text-2-2-2">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a0522d;">E_nn</span> = trexio.read_nucleus_repulsion(f)
@ -955,8 +955,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org6356182" class="outline-4">
<h4 id="org6356182"><span class="section-number-4">2.2.3</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org3a3c6da" class="outline-4">
<h4 id="org3a3c6da"><span class="section-number-4">2.2.3</span> Read the number of molecular orbitals</h4>
<div class="outline-text-4" id="text-2-2-3">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a0522d;">n</span> = trexio.read_mo_num(f)
@ -965,8 +965,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-orgcf7575b" class="outline-4">
<h4 id="orgcf7575b"><span class="section-number-4">2.2.4</span> Read one-electron quantities</h4>
<div id="outline-container-org21c880d" class="outline-4">
<h4 id="org21c880d"><span class="section-number-4">2.2.4</span> Read one-electron quantities</h4>
<div class="outline-text-4" id="text-2-2-4">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">if</span> <span style="color: #a020f0;">not</span> trexio.has_mo_1e_int_core_hamiltonian(f):
@ -985,12 +985,12 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-orge4cf3ec" class="outline-4">
<h4 id="orge4cf3ec"><span class="section-number-4">2.2.5</span> Read two-electron quantities</h4>
<div id="outline-container-orgb70a042" class="outline-4">
<h4 id="orgb70a042"><span class="section-number-4">2.2.5</span> Read two-electron quantities</h4>
<div class="outline-text-4" id="text-2-2-5">
</div>
<div id="outline-container-org8903f8c" class="outline-5">
<h5 id="org8903f8c"><span class="section-number-5">2.2.5.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org1c6c12a" class="outline-5">
<h5 id="org1c6c12a"><span class="section-number-5">2.2.5.1</span> Electron repulsion integrals</h5>
<div class="outline-text-5" id="text-2-2-5-1">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">if</span> <span style="color: #a020f0;">not</span> trexio.has_mo_2e_int_eri(f):
@ -1020,8 +1020,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org8b30e36" class="outline-5">
<h5 id="org8b30e36"><span class="section-number-5">2.2.5.2</span> Reduced density matrix</h5>
<div id="outline-container-org1ca360f" class="outline-5">
<h5 id="org1ca360f"><span class="section-number-5">2.2.5.2</span> Reduced density matrix</h5>
<div class="outline-text-5" id="text-2-2-5-2">
<div class="org-src-container">
<pre class="src src-python"><span style="color: #a020f0;">if</span> <span style="color: #a020f0;">not</span> trexio.has_rdm_2e(f):
@ -1043,8 +1043,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org85b6c2f" class="outline-4">
<h4 id="org85b6c2f"><span class="section-number-4">2.2.6</span> Compute the energy</h4>
<div id="outline-container-orgd0b7298" class="outline-4">
<h4 id="orgd0b7298"><span class="section-number-4">2.2.6</span> Compute the energy</h4>
<div class="outline-text-4" id="text-2-2-6">
<p>
When the orbitals are real, we can use
@ -1073,12 +1073,12 @@ E &=& E_{\text{NN}} + \sum_{ij} \gamma_{ij}\, \langle j | h | i \rangle\,
</div>
</div>
<div id="outline-container-orge257625" class="outline-2">
<h2 id="orge257625"><span class="section-number-2">3</span> Reading determinants</h2>
<div id="outline-container-org20dedfe" class="outline-2">
<h2 id="org20dedfe"><span class="section-number-2">3</span> Reading determinants</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org336aefc" class="outline-3">
<h3 id="org336aefc"><span class="section-number-3">3.1</span> Fortran</h3>
<div id="outline-container-org3ff3b43" class="outline-3">
<h3 id="org3ff3b43"><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>
@ -1157,7 +1157,7 @@ end
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-12-13 Wed 10:07</p>
<p class="date">Created: 2024-01-11 Thu 15:02</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

4
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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>
<!-- 2023-12-13 Wed 10:07 -->
<!-- 2024-01-11 Thu 15:02 -->
<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>
@ -406,7 +406,7 @@ 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: 2023-12-13 Wed 10:07</p>
<p class="date">Created: 2024-01-11 Thu 15:02</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

4
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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>
<!-- 2023-12-13 Wed 10:07 -->
<!-- 2024-01-11 Thu 15:02 -->
<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: 2023-12-13 Wed 10:07</p>
<p class="date">Created: 2024-01-11 Thu 15:02</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

58
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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>
<!-- 2023-12-13 Wed 10:07 -->
<!-- 2024-01-11 Thu 15:02 -->
<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="#orgcec7cb2">1. Format specification</a>
<li><a href="#org5fbcbc8">1. Format specification</a>
<ul>
<li><a href="#orgc1dd695">1.1. Organization of the data</a></li>
<li><a href="#org6cb9158">1.2. Data types</a></li>
<li><a href="#orga8caad6">1.1. Organization of the data</a></li>
<li><a href="#org7cf16aa">1.2. Data types</a></li>
</ul>
</li>
<li><a href="#orge698172">2. The TREXIO library</a>
<li><a href="#orgea267ae">2. The TREXIO library</a>
<ul>
<li><a href="#org2cf373f">2.1. The front-end</a></li>
<li><a href="#orgb3a6507">2.2. The back-end</a></li>
<li><a href="#orgd0a09ac">2.3. Supported languages</a></li>
<li><a href="#org4c40787">2.4. Source code generation and documentation</a></li>
<li><a href="#org7849e25">2.5. Availability</a></li>
<li><a href="#orge0b13db">2.1. The front-end</a></li>
<li><a href="#org1e03288">2.2. The back-end</a></li>
<li><a href="#orgf3b794a">2.3. Supported languages</a></li>
<li><a href="#org9479802">2.4. Source code generation and documentation</a></li>
<li><a href="#orgd3ff8db">2.5. Availability</a></li>
</ul>
</li>
</ul>
@ -366,8 +366,8 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-orgcec7cb2" class="outline-2">
<h2 id="orgcec7cb2"><span class="section-number-2">1</span> Format specification</h2>
<div id="outline-container-org5fbcbc8" class="outline-2">
<h2 id="org5fbcbc8"><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-orgc1dd695" class="outline-3">
<h3 id="orgc1dd695"><span class="section-number-3">1.1</span> Organization of the data</h3>
<div id="outline-container-orga8caad6" class="outline-3">
<h3 id="orga8caad6"><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-org6cb9158" class="outline-3">
<h3 id="org6cb9158"><span class="section-number-3">1.2</span> Data types</h3>
<div id="outline-container-org7cf16aa" class="outline-3">
<h3 id="org7cf16aa"><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-orge698172" class="outline-2">
<h2 id="orge698172"><span class="section-number-2">2</span> The TREXIO library</h2>
<div id="outline-container-orgea267ae" class="outline-2">
<h2 id="orgea267ae"><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-org2cf373f" class="outline-3">
<h3 id="org2cf373f"><span class="section-number-3">2.1</span> The front-end</h3>
<div id="outline-container-orge0b13db" class="outline-3">
<h3 id="orge0b13db"><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-orgb3a6507" class="outline-3">
<h3 id="orgb3a6507"><span class="section-number-3">2.2</span> The back-end</h3>
<div id="outline-container-org1e03288" class="outline-3">
<h3 id="org1e03288"><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-orgd0a09ac" class="outline-3">
<h3 id="orgd0a09ac"><span class="section-number-3">2.3</span> Supported languages</h3>
<div id="outline-container-orgf3b794a" class="outline-3">
<h3 id="orgf3b794a"><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-org4c40787" class="outline-3">
<h3 id="org4c40787"><span class="section-number-3">2.4</span> Source code generation and documentation</h3>
<div id="outline-container-org9479802" class="outline-3">
<h3 id="org9479802"><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-org7849e25" class="outline-3">
<h3 id="org7849e25"><span class="section-number-3">2.5</span> Availability</h3>
<div id="outline-container-orgd3ff8db" class="outline-3">
<h3 id="orgd3ff8db"><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: 2023-12-13 Wed 10:07</p>
<p class="date">Created: 2024-01-11 Thu 15:02</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>
<!-- 2023-12-13 Wed 10:06 -->
<!-- 2024-01-11 Thu 15:02 -->
<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="#org2e0de39">1. Template for HDF5 definitions</a></li>
<li><a href="#org3c0b694">2. Template for HDF5 structures</a></li>
<li><a href="#org88f8288">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org772f606">4. Template for HDF5 has a group</a></li>
<li><a href="#org8762d14">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org32c47bb">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org8ae80c7">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#orgd1c1fe2">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#orgbc5b35f">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org4b05bf9">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org65612d3">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#orga1443f5">12. Source code for the determinant part</a></li>
<li><a href="#org0e073fc">13. Helper functions</a></li>
<li><a href="#org196da00">1. Template for HDF5 definitions</a></li>
<li><a href="#orgeb09198">2. Template for HDF5 structures</a></li>
<li><a href="#orga758412">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgf1b64c2">4. Template for HDF5 has a group</a></li>
<li><a href="#orgaa2eab5">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orgd317626">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org8469e18">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#orgf63133e">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#orgaafcbbe">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#orgdbe1f51">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org676585d">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org1cdebfe">12. Source code for the determinant part</a></li>
<li><a href="#org1bde160">13. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-org2e0de39" class="outline-2">
<h2 id="org2e0de39"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-org196da00" class="outline-2">
<h2 id="org196da00"><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-org3c0b694" class="outline-2">
<h2 id="org3c0b694"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-orgeb09198" class="outline-2">
<h2 id="orgeb09198"><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-org88f8288" class="outline-2">
<h2 id="org88f8288"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-orga758412" class="outline-2">
<h2 id="orga758412"><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-org772f606" class="outline-2">
<h2 id="org772f606"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-orgf1b64c2" class="outline-2">
<h2 id="orgf1b64c2"><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-org8762d14" class="outline-2">
<h2 id="org8762d14"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-orgaa2eab5" class="outline-2">
<h2 id="orgaa2eab5"><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-org32c47bb" class="outline-2">
<h2 id="org32c47bb"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-orgd317626" class="outline-2">
<h2 id="orgd317626"><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-org8ae80c7" class="outline-2">
<h2 id="org8ae80c7"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-org8469e18" class="outline-2">
<h2 id="org8469e18"><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
@ -976,8 +976,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-orgd1c1fe2" class="outline-2">
<h2 id="orgd1c1fe2"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div id="outline-container-orgf63133e" class="outline-2">
<h2 id="orgf63133e"><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.
@ -1111,8 +1111,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
<div id="outline-container-orgbc5b35f" class="outline-2">
<h2 id="orgbc5b35f"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-orgaafcbbe" class="outline-2">
<h2 id="orgaafcbbe"><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>
@ -1309,8 +1309,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
<div id="outline-container-org4b05bf9" class="outline-2">
<h2 id="org4b05bf9"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-orgdbe1f51" class="outline-2">
<h2 id="orgdbe1f51"><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>
@ -1437,8 +1437,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
</div>
<div id="outline-container-org65612d3" class="outline-2">
<h2 id="org65612d3"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-org676585d" class="outline-2">
<h2 id="org676585d"><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
@ -1478,8 +1478,8 @@ Thus, any corrupted/lost file space will remain in the first file. The use of <c
</div>
</div>
<div id="outline-container-orga1443f5" class="outline-2">
<h2 id="orga1443f5"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div id="outline-container-org1cdebfe" class="outline-2">
<h2 id="org1cdebfe"><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.
@ -1581,8 +1581,8 @@ Size specifies the number of data items (e.g. determinants) to process.
</div>
</div>
<div id="outline-container-org0e073fc" class="outline-2">
<h2 id="org0e073fc"><span class="section-number-2">13</span> Helper functions</h2>
<div id="outline-container-org1bde160" class="outline-2">
<h2 id="org1bde160"><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>
@ -1850,7 +1850,7 @@ 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: 2023-12-13 Wed 10:06</p>
<p class="date">Created: 2024-01-11 Thu 15:02</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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<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="#org384e8be">1. Template for group-related structures in text back end</a></li>
<li><a href="#orgcc3dc0d">2. Template for general structure in text back end</a></li>
<li><a href="#org134d4f9">3. Initialize function (constant part)</a></li>
<li><a href="#org6c3610f">4. Deinitialize function (templated part)</a></li>
<li><a href="#org9a6cf94">5. Flush function (templated part)</a></li>
<li><a href="#orgeb95b86">6. Template for text read a group</a></li>
<li><a href="#orgda6cdd0">7. Template for text has a group</a></li>
<li><a href="#orgd52e553">8. Template for text flush a group</a></li>
<li><a href="#orgd83a766">9. Template for text free memory</a></li>
<li><a href="#org2d01da0">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org2d5c414">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org95563df">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orgf524b20">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org87e166e">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org6c3bb62">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#orgbbc700c">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#orga1f35b0">17. Source code for the determinant part</a></li>
<li><a href="#org921c7ca">1. Template for group-related structures in text back end</a></li>
<li><a href="#orgfb3fe7b">2. Template for general structure in text back end</a></li>
<li><a href="#orgd4bb3e2">3. Initialize function (constant part)</a></li>
<li><a href="#org639d0d6">4. Deinitialize function (templated part)</a></li>
<li><a href="#org935264b">5. Flush function (templated part)</a></li>
<li><a href="#orgfa59e49">6. Template for text read a group</a></li>
<li><a href="#orge838c79">7. Template for text has a group</a></li>
<li><a href="#org9d763c0">8. Template for text flush a group</a></li>
<li><a href="#org8fd9882">9. Template for text free memory</a></li>
<li><a href="#orga550619">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org087c867">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orgdcb405b">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org7b9dad5">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org535ad55">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org7df059b">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org2b026f9">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org7a9de96">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-org384e8be" class="outline-2">
<h2 id="org384e8be"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-org921c7ca" class="outline-2">
<h2 id="org921c7ca"><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-orgcc3dc0d" class="outline-2">
<h2 id="orgcc3dc0d"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-orgfb3fe7b" class="outline-2">
<h2 id="orgfb3fe7b"><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-org134d4f9" class="outline-2">
<h2 id="org134d4f9"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-orgd4bb3e2" class="outline-2">
<h2 id="orgd4bb3e2"><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>
@ -601,8 +601,8 @@ In that case, we define an alternate one, which is not as safe as the original o
</div>
</div>
<div id="outline-container-org6c3610f" class="outline-2">
<h2 id="org6c3610f"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-org639d0d6" class="outline-2">
<h2 id="org639d0d6"><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>
@ -624,8 +624,8 @@ In that case, we define an alternate one, which is not as safe as the original o
</div>
</div>
<div id="outline-container-org9a6cf94" class="outline-2">
<h2 id="org9a6cf94"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div id="outline-container-org935264b" class="outline-2">
<h2 id="org935264b"><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>
@ -648,8 +648,8 @@ In that case, we define an alternate one, which is not as safe as the original o
</div>
</div>
<div id="outline-container-orgeb95b86" class="outline-2">
<h2 id="orgeb95b86"><span class="section-number-2">6</span> Template for text read a group</h2>
<div id="outline-container-orgfa59e49" class="outline-2">
<h2 id="orgfa59e49"><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*
@ -875,8 +875,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-orgda6cdd0" class="outline-2">
<h2 id="orgda6cdd0"><span class="section-number-2">7</span> Template for text has a group</h2>
<div id="outline-container-orge838c79" class="outline-2">
<h2 id="orge838c79"><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>
@ -916,8 +916,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-orgd52e553" class="outline-2">
<h2 id="orgd52e553"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div id="outline-container-org9d763c0" class="outline-2">
<h2 id="org9d763c0"><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>
@ -981,8 +981,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-orgd83a766" class="outline-2">
<h2 id="orgd83a766"><span class="section-number-2">9</span> Template for text free memory</h2>
<div id="outline-container-org8fd9882" class="outline-2">
<h2 id="org8fd9882"><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.
@ -1051,8 +1051,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-org2d01da0" class="outline-2">
<h2 id="org2d01da0"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-orga550619" class="outline-2">
<h2 id="orga550619"><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>
@ -1115,8 +1115,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-org2d5c414" class="outline-2">
<h2 id="org2d5c414"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-org087c867" class="outline-2">
<h2 id="org087c867"><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.
@ -1212,8 +1212,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org95563df" class="outline-2">
<h2 id="org95563df"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-orgdcb405b" class="outline-2">
<h2 id="orgdcb405b"><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.
@ -1314,8 +1314,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-orgf524b20" class="outline-2">
<h2 id="orgf524b20"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-org7b9dad5" class="outline-2">
<h2 id="org7b9dad5"><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>
@ -1389,8 +1389,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org87e166e" class="outline-2">
<h2 id="org87e166e"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-org535ad55" class="outline-2">
<h2 id="org535ad55"><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
@ -1680,8 +1680,8 @@ User provides indices and values of the sparse array as two separate variables.
</div>
</div>
<div id="outline-container-org6c3bb62" class="outline-2">
<h2 id="org6c3bb62"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div id="outline-container-org7df059b" class="outline-2">
<h2 id="org7df059b"><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
@ -1911,8 +1911,8 @@ Size specifies the number of vector elements to be written.
</div>
</div>
</div>
<div id="outline-container-orgbbc700c" class="outline-2">
<h2 id="orgbbc700c"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-org2b026f9" class="outline-2">
<h2 id="org2b026f9"><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>
@ -1940,8 +1940,8 @@ Size specifies the number of vector elements to be written.
</div>
</div>
<div id="outline-container-orga1f35b0" class="outline-2">
<h2 id="orga1f35b0"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div id="outline-container-org7a9de96" class="outline-2">
<h2 id="org7a9de96"><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
@ -2133,7 +2133,7 @@ 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: 2023-12-13 Wed 10:07</p>
<p class="date">Created: 2024-01-11 Thu 15:02</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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<head>
<!-- 2023-12-13 Wed 10:07 -->
<!-- 2024-01-11 Thu 15:02 -->
<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>
@ -346,71 +346,71 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org0454c22">1. Metadata (metadata group)</a></li>
<li><a href="#orgbba67e6">2. System</a>
<li><a href="#org12c394d">1. Metadata (metadata group)</a></li>
<li><a href="#org76fe14d">2. System</a>
<ul>
<li><a href="#org21b61f6">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org14287e6">2.2. Cell (cell group)</a></li>
<li><a href="#orga04de99">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org57d5938">2.4. Electron (electron group)</a></li>
<li><a href="#orgcdbab2a">2.5. Ground or excited states (state group)</a></li>
<li><a href="#orgd0fd537">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org8969537">2.2. Cell (cell group)</a></li>
<li><a href="#org264eb83">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org3b5f092">2.4. Electron (electron group)</a></li>
<li><a href="#orgcad0d93">2.5. Ground or excited states (state group)</a></li>
</ul>
</li>
<li><a href="#orgcff4d12">3. Basis functions</a>
<li><a href="#orgc707a00">3. Basis functions</a>
<ul>
<li><a href="#org1958a86">3.1. Basis set (basis group)</a>
<li><a href="#org589da67">3.1. Basis set (basis group)</a>
<ul>
<li><a href="#org4b34cd4">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#orgb1b08ff">3.1.2. Numerical orbitals</a></li>
<li><a href="#orgf5b2878">3.1.3. Plane waves</a></li>
<li><a href="#org8a7e0e7">3.1.4. Data definitions</a></li>
<li><a href="#orgd080ebe">3.1.5. Example</a></li>
<li><a href="#org68ed7f8">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#orgfedbeca">3.1.2. Numerical orbitals</a></li>
<li><a href="#org72ffaea">3.1.3. Plane waves</a></li>
<li><a href="#org6cc6216">3.1.4. Data definitions</a></li>
<li><a href="#orgc5cfcb6">3.1.5. Example</a></li>
</ul>
</li>
<li><a href="#orgcf0efbc">3.2. Effective core potentials (ecp group)</a>
<li><a href="#org30fbe84">3.2. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org63ba606">3.2.1. Example</a></li>
<li><a href="#orgbd11093">3.2.1. Example</a></li>
</ul>
</li>
<li><a href="#org4046d85">3.3. Numerical integration grid (grid group)</a></li>
<li><a href="#org5c9c54e">3.3. Numerical integration grid (grid group)</a></li>
</ul>
</li>
<li><a href="#orgf4827cd">4. Orbitals</a>
<li><a href="#org83cfbc2">4. Orbitals</a>
<ul>
<li><a href="#orgd553ac6">4.1. Atomic orbitals (ao group)</a>
<li><a href="#org87edc32">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="#orgddd6de2">4.2. Molecular orbitals (mo group)</a>
<li><a href="#org63f91e7">4.2. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org8b52f09">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org25d4658">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org8add549">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org724bdb3">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org0f2225e">5. Multi-determinant information</a>
<li><a href="#org3084e9b">5. Multi-determinant information</a>
<ul>
<li><a href="#org5f0f387">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#orgfce0bda">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#org36ec0bb">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org2db5cc0">5.4. Reduced density matrices (rdm group)</a></li>
<li><a href="#orgbac9a0e">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org6887b13">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#org951d104">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org8b45c11">5.4. Reduced density matrices (rdm group)</a></li>
</ul>
</li>
<li><a href="#org7da6180">6. Correlation factors</a>
<li><a href="#orgc27ec7a">6. Correlation factors</a>
<ul>
<li><a href="#orge8b5f04">6.1. Jastrow factor (jastrow group)</a>
<li><a href="#orgdd551b3">6.1. Jastrow factor (jastrow group)</a>
<ul>
<li><a href="#orgf3afbc8">6.1.1. CHAMP</a></li>
<li><a href="#org69df6f1">6.1.2. Mu</a></li>
<li><a href="#org32c4a9a">6.1.3. Table of values</a></li>
<li><a href="#org1b8aa22">6.1.1. CHAMP</a></li>
<li><a href="#orgc227e51">6.1.2. Mu</a></li>
<li><a href="#org985966d">6.1.3. Table of values</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org716521a">7. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#org2452fab">7. Quantum Monte Carlo data (qmc group)</a></li>
</ul>
</div>
</div>
@ -423,8 +423,8 @@ is reversed in the produced <code>trex.json</code> configuration file as the
library is written in C.
</p>
<div id="outline-container-org0454c22" class="outline-2">
<h2 id="org0454c22"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org12c394d" class="outline-2">
<h2 id="org12c394d"><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,
@ -434,7 +434,7 @@ have participated to the creation of the file, a list of authors of
the file, and a textual description.
</p>
<table id="org7c4571e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb25bfd1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -517,19 +517,19 @@ value can be manually overwritten (in unsafe mode) from <code>1</code> to <code>
</div>
</div>
<div id="outline-container-orgbba67e6" class="outline-2">
<h2 id="orgbba67e6"><span class="section-number-2">2</span> System</h2>
<div id="outline-container-org76fe14d" class="outline-2">
<h2 id="org76fe14d"><span class="section-number-2">2</span> System</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org21b61f6" class="outline-3">
<h3 id="org21b61f6"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
<div id="outline-container-orgd0fd537" class="outline-3">
<h3 id="orgd0fd537"><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="org9b2ea0f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org0be5ef5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -596,15 +596,15 @@ given in Cartesian \((x,y,z)\) format.
</div>
</div>
<div id="outline-container-org14287e6" class="outline-3">
<h3 id="org14287e6"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
<div id="outline-container-org8969537" class="outline-3">
<h3 id="org8969537"><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="orgb0c191c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgfe83ff8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -678,15 +678,15 @@ used in periodic calculations.
</div>
</div>
<div id="outline-container-orga04de99" class="outline-3">
<h3 id="orga04de99"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div id="outline-container-org264eb83" class="outline-3">
<h3 id="org264eb83"><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="org243037c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga876a74" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -725,8 +725,8 @@ defined in this group.
</div>
</div>
<div id="outline-container-org57d5938" class="outline-3">
<h3 id="org57d5938"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
<div id="outline-container-org3b5f092" class="outline-3">
<h3 id="org3b5f092"><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
@ -745,7 +745,7 @@ the number of &uarr; and &darr; electrons is fixed.
</p>
<table id="org4bf7496" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgbd4ba57" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -791,8 +791,8 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-orgcdbab2a" class="outline-3">
<h3 id="orgcdbab2a"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
<div id="outline-container-orgcad0d93" class="outline-3">
<h3 id="orgcad0d93"><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
@ -809,7 +809,7 @@ integrals, etc.
The <code>id</code> and <code>current_label</code> attributes need to be specified for each file.
</p>
<table id="org351d664" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgcd9ab1e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -877,16 +877,16 @@ The <code>id</code> and <code>current_label</code> attributes need to be specifi
</div>
</div>
<div id="outline-container-orgcff4d12" class="outline-2">
<h2 id="orgcff4d12"><span class="section-number-2">3</span> Basis functions</h2>
<div id="outline-container-orgc707a00" class="outline-2">
<h2 id="orgc707a00"><span class="section-number-2">3</span> Basis functions</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org1958a86" class="outline-3">
<h3 id="org1958a86"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
<div id="outline-container-org589da67" class="outline-3">
<h3 id="org589da67"><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-org4b34cd4" class="outline-4">
<h4 id="org4b34cd4"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
<div id="outline-container-org68ed7f8" class="outline-4">
<h4 id="org68ed7f8"><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
@ -940,8 +940,8 @@ All the basis set parameters are stored in one-dimensional arrays.
</div>
</div>
<div id="outline-container-orgb1b08ff" class="outline-4">
<h4 id="orgb1b08ff"><span class="section-number-4">3.1.2</span> Numerical orbitals</h4>
<div id="outline-container-orgfedbeca" class="outline-4">
<h4 id="orgfedbeca"><span class="section-number-4">3.1.2</span> Numerical orbitals</h4>
<div class="outline-text-4" id="text-3-1-2">
<p>
Trexio supports numerical atom centered orbitals. The implementation is
@ -1005,8 +1005,8 @@ reimplement them with consideration for its specific needs.
</div>
</div>
<div id="outline-container-orgf5b2878" class="outline-4">
<h4 id="orgf5b2878"><span class="section-number-4">3.1.3</span> Plane waves</h4>
<div id="outline-container-org72ffaea" class="outline-4">
<h4 id="org72ffaea"><span class="section-number-4">3.1.3</span> Plane waves</h4>
<div class="outline-text-4" id="text-3-1-3">
<p>
A plane wave is defined as
@ -1027,10 +1027,10 @@ plane waves.
</div>
</div>
<div id="outline-container-org8a7e0e7" class="outline-4">
<h4 id="org8a7e0e7"><span class="section-number-4">3.1.4</span> Data definitions</h4>
<div id="outline-container-org6cc6216" class="outline-4">
<h4 id="org6cc6216"><span class="section-number-4">3.1.4</span> Data definitions</h4>
<div class="outline-text-4" id="text-3-1-4">
<table id="org5d5cffc" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2cf0da9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1250,8 +1250,8 @@ plane waves.
</div>
</div>
<div id="outline-container-orgd080ebe" class="outline-4">
<h4 id="orgd080ebe"><span class="section-number-4">3.1.5</span> Example</h4>
<div id="outline-container-orgc5cfcb6" class="outline-4">
<h4 id="orgc5cfcb6"><span class="section-number-4">3.1.5</span> Example</h4>
<div class="outline-text-4" id="text-3-1-5">
<p>
For example, consider H<sub>2</sub> with the following basis set (in GAMESS
@ -1329,8 +1329,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-orgcf0efbc" class="outline-3">
<h3 id="orgcf0efbc"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
<div id="outline-container-org30fbe84" class="outline-3">
<h3 id="org30fbe84"><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
@ -1364,7 +1364,7 @@ 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="org17da32f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org8729797" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1468,8 +1468,8 @@ If you encounter the aforementioned issue, please report it to our
</p>
</div>
<div id="outline-container-org63ba606" class="outline-4">
<h4 id="org63ba606"><span class="section-number-4">3.2.1</span> Example</h4>
<div id="outline-container-orgbd11093" class="outline-4">
<h4 id="orgbd11093"><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
@ -1532,8 +1532,8 @@ power = [
</div>
</div>
<div id="outline-container-org4046d85" class="outline-3">
<h3 id="org4046d85"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
<div id="outline-container-org5c9c54e" class="outline-3">
<h3 id="org5c9c54e"><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
@ -1548,7 +1548,7 @@ 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="org6ad49e3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgfaa4d7c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1665,12 +1665,12 @@ Feel free to submit a PR if you find missing options/functionalities.
</div>
</div>
<div id="outline-container-orgf4827cd" class="outline-2">
<h2 id="orgf4827cd"><span class="section-number-2">4</span> Orbitals</h2>
<div id="outline-container-org83cfbc2" class="outline-2">
<h2 id="org83cfbc2"><span class="section-number-2">4</span> Orbitals</h2>
<div class="outline-text-2" id="text-4">
</div>
<div id="outline-container-orgd553ac6" class="outline-3">
<h3 id="orgd553ac6"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
<div id="outline-container-org87edc32" class="outline-3">
<h3 id="org87edc32"><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
@ -1751,7 +1751,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</p>
<table id="orgbc21b50" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga8f4fb2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1803,7 +1803,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</table>
</div>
<div id="outline-container-orgca137f8" class="outline-4">
<div id="outline-container-org563de75" 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">
@ -1821,7 +1821,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="org66fcd45" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org199c7c7" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1916,7 +1916,7 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-orgb2bf069" class="outline-4">
<div id="outline-container-org6cd0411" 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>
@ -1942,7 +1942,7 @@ The Cholesky decomposition of the integrals can also be stored:
\]
</p>
<table id="org5a4f0ec" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2c850d9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2010,10 +2010,10 @@ The Cholesky decomposition of the integrals can also be stored:
</div>
</div>
<div id="outline-container-orgddd6de2" class="outline-3">
<h3 id="orgddd6de2"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div id="outline-container-org63f91e7" class="outline-3">
<h3 id="org63f91e7"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div class="outline-text-3" id="text-4-2">
<table id="orga33ec26" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org025cfd6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2100,8 +2100,8 @@ The Cholesky decomposition of the integrals can also be stored:
</table>
</div>
<div id="outline-container-org8b52f09" class="outline-4">
<h4 id="org8b52f09"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
<div id="outline-container-org8add549" class="outline-4">
<h4 id="org8add549"><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
@ -2109,7 +2109,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org632f019" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgbabcbbe" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2204,8 +2204,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org25d4658" class="outline-4">
<h4 id="org25d4658"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
<div id="outline-container-org724bdb3" class="outline-4">
<h4 id="org724bdb3"><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
@ -2213,7 +2213,7 @@ The operators are the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org7154859" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc652e3b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2282,12 +2282,12 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org0f2225e" class="outline-2">
<h2 id="org0f2225e"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div id="outline-container-org3084e9b" class="outline-2">
<h2 id="org3084e9b"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div class="outline-text-2" id="text-5">
</div>
<div id="outline-container-org5f0f387" class="outline-3">
<h3 id="org5f0f387"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
<div id="outline-container-orgbac9a0e" class="outline-3">
<h3 id="orgbac9a0e"><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 \(\Psi\)
@ -2329,7 +2329,7 @@ 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="org72d2d8a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org9c47b84" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2375,8 +2375,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
</div>
</div>
<div id="outline-container-orgfce0bda" class="outline-3">
<h3 id="orgfce0bda"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
<div id="outline-container-org6887b13" class="outline-3">
<h3 id="org6887b13"><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
@ -2398,7 +2398,7 @@ matrix \(\langle D_I | \psi_J \rangle\) needed to project the CSFs in
the basis of Slater determinants.
</p>
<table id="orge808192" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org6bc962a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2444,8 +2444,8 @@ the basis of Slater determinants.
</div>
</div>
<div id="outline-container-org36ec0bb" class="outline-3">
<h3 id="org36ec0bb"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
<div id="outline-container-org951d104" class="outline-3">
<h3 id="org951d104"><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
@ -2516,7 +2516,7 @@ The order of the indices is chosen such that
<li>\(\dots\)</li>
</ul>
<table id="org1b64500" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga59afe8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2597,8 +2597,8 @@ The order of the indices is chosen such that
</div>
</div>
<div id="outline-container-org2db5cc0" class="outline-3">
<h3 id="org2db5cc0"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
<div id="outline-container-org8b45c11" class="outline-3">
<h3 id="org8b45c11"><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
@ -2670,7 +2670,7 @@ 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="org1376f17" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org12bff8b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2801,12 +2801,12 @@ expressed in a basis of a one-electron function
</div>
</div>
<div id="outline-container-org7da6180" class="outline-2">
<h2 id="org7da6180"><span class="section-number-2">6</span> Correlation factors</h2>
<div id="outline-container-orgc27ec7a" class="outline-2">
<h2 id="orgc27ec7a"><span class="section-number-2">6</span> Correlation factors</h2>
<div class="outline-text-2" id="text-6">
</div>
<div id="outline-container-orge8b5f04" class="outline-3">
<h3 id="orge8b5f04"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
<div id="outline-container-orgdd551b3" class="outline-3">
<h3 id="orgdd551b3"><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
@ -2831,8 +2831,8 @@ following:
</ul>
</div>
<div id="outline-container-orgf3afbc8" class="outline-4">
<h4 id="orgf3afbc8"><span class="section-number-4">6.1.1</span> CHAMP</h4>
<div id="outline-container-org1b8aa22" class="outline-4">
<h4 id="org1b8aa22"><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
@ -2933,8 +2933,8 @@ The terms \(J_{\text{ee},ij}^\infty\) and \(J_{\text{eN}}^\infty\) are shifts to
</div>
<div id="outline-container-org69df6f1" class="outline-4">
<h4 id="org69df6f1"><span class="section-number-4">6.1.2</span> Mu</h4>
<div id="outline-container-orgc227e51" class="outline-4">
<h4 id="orgc227e51"><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
@ -3031,10 +3031,10 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
</div>
</div>
<div id="outline-container-org32c4a9a" class="outline-4">
<h4 id="org32c4a9a"><span class="section-number-4">6.1.3</span> Table of values</h4>
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<h4 id="org985966d"><span class="section-number-4">6.1.3</span> Table of values</h4>
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@ -3138,8 +3138,8 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
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<h2 id="org716521a"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
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<h2 id="org2452fab"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
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In quantum Monte Carlo calculations, the wave function is evaluated
@ -3153,7 +3153,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
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@ -3208,7 +3208,7 @@ of $&uarr;$-spin and then all the $&darr;$-spin.
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<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-12-13 Wed 10:07</p>
<p class="date">Created: 2024-01-11 Thu 15:02</p>
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