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README.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>
<!-- 2024-03-13 Wed 13:26 -->
<!-- 2024-03-15 Fri 12:21 -->
<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: 2024-03-13 Wed 13:26</p>
<p class="date">Created: 2024-03-15 Fri 12:21</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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examples.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>
<!-- 2024-03-13 Wed 13:26 -->
<!-- 2024-03-15 Fri 12:21 -->
<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="#orge26d9d0">1. Writing nuclear coordinates</a>
<li><a href="#orgbd301a4">1. Writing nuclear coordinates</a>
<ul>
<li><a href="#org7700984">1.1. C</a></li>
<li><a href="#org9112f51">1.2. Python</a></li>
<li><a href="#orga41ec17">1.3. Fortran</a></li>
<li><a href="#org7b636c2">1.1. C</a></li>
<li><a href="#org2b9e612">1.2. Python</a></li>
<li><a href="#orgacbe867">1.3. Fortran</a></li>
</ul>
</li>
<li><a href="#org2582a84">2. Accessing sparse quantities (integrals)</a>
<li><a href="#orgad438c4">2. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#org30c0248">2.1. Fortran</a>
<li><a href="#org3cbb608">2.1. Fortran</a>
<ul>
<li><a href="#orge0e1a01">2.1.1. Declare Temporary variables</a></li>
<li><a href="#org5140957">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgf37b5b9">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org7cb5c49">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org98d9d6d">2.1.5. Allocate memory</a></li>
<li><a href="#orgf0ee13e">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org9af9468">2.1.7. Read two-electron quantities</a>
<li><a href="#org9daf7a9">2.1.1. Declare Temporary variables</a></li>
<li><a href="#org975b352">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgefd500f">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org157169e">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org6edf345">2.1.5. Allocate memory</a></li>
<li><a href="#org8b35980">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org7e10529">2.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org2e823bc">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org366cb7a">2.1.7.2. Reduced density matrix</a></li>
<li><a href="#org0d88176">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#orgaf064f0">2.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org006858c">2.1.8. Compute the energy</a></li>
<li><a href="#orgdb059f1">2.1.9. Terminate</a></li>
<li><a href="#org43b2563">2.1.8. Compute the energy</a></li>
<li><a href="#org0180ebc">2.1.9. Terminate</a></li>
</ul>
</li>
<li><a href="#org788ae8f">2.2. Python</a>
<li><a href="#org9335654">2.2. Python</a>
<ul>
<li><a href="#org839c315">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org617c079">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#org0bfcf25">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#org3e8c412">2.2.4. Read one-electron quantities</a></li>
<li><a href="#org53dee91">2.2.5. Read two-electron quantities</a>
<li><a href="#orgd61911c">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org0e4ba0b">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#org080ee21">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#org9b99901">2.2.4. Read one-electron quantities</a></li>
<li><a href="#org9fd1bf4">2.2.5. Read two-electron quantities</a>
<ul>
<li><a href="#orgfacc0aa">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#orgac750a9">2.2.5.2. Reduced density matrix</a></li>
<li><a href="#org76cfe1b">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#org7681f76">2.2.5.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#orgf50ad96">2.2.6. Compute the energy</a></li>
<li><a href="#orgd8e797e">2.2.6. Compute the energy</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orge8a0de0">3. Reading determinants</a>
<li><a href="#org6cb4cd7">3. Reading determinants</a>
<ul>
<li><a href="#org2d425c8">3.1. Fortran</a></li>
<li><a href="#orga91a87f">3.1. Fortran</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-orge26d9d0" class="outline-2">
<h2 id="orge26d9d0"><span class="section-number-2">1</span> Writing nuclear coordinates</h2>
<div id="outline-container-orgbd301a4" class="outline-2">
<h2 id="orgbd301a4"><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-org7700984" class="outline-3">
<h3 id="org7700984"><span class="section-number-3">1.1</span> C</h3>
<div id="outline-container-org7b636c2" class="outline-3">
<h3 id="org7b636c2"><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-org9112f51" class="outline-3">
<h3 id="org9112f51"><span class="section-number-3">1.2</span> Python</h3>
<div id="outline-container-org2b9e612" class="outline-3">
<h3 id="org2b9e612"><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-orga41ec17" class="outline-3">
<h3 id="orga41ec17"><span class="section-number-3">1.3</span> Fortran</h3>
<div id="outline-container-orgacbe867" class="outline-3">
<h3 id="orgacbe867"><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-org2582a84" class="outline-2">
<h2 id="org2582a84"><span class="section-number-2">2</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-orgad438c4" class="outline-2">
<h2 id="orgad438c4"><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-org30c0248" class="outline-3">
<h3 id="org30c0248"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-org3cbb608" class="outline-3">
<h3 id="org3cbb608"><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-orge0e1a01" class="outline-4">
<h4 id="orge0e1a01"><span class="section-number-4">2.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org9daf7a9" class="outline-4">
<h4 id="org9daf7a9"><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-org5140957" class="outline-4">
<h4 id="org5140957"><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-org975b352" class="outline-4">
<h4 id="org975b352"><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-orgf37b5b9" class="outline-4">
<h4 id="orgf37b5b9"><span class="section-number-4">2.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orgefd500f" class="outline-4">
<h4 id="orgefd500f"><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-org7cb5c49" class="outline-4">
<h4 id="org7cb5c49"><span class="section-number-4">2.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org157169e" class="outline-4">
<h4 id="org157169e"><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-org98d9d6d" class="outline-4">
<h4 id="org98d9d6d"><span class="section-number-4">2.1.5</span> Allocate memory</h4>
<div id="outline-container-org6edf345" class="outline-4">
<h4 id="org6edf345"><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-orgf0ee13e" class="outline-4">
<h4 id="orgf0ee13e"><span class="section-number-4">2.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org8b35980" class="outline-4">
<h4 id="org8b35980"><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-org9af9468" class="outline-4">
<h4 id="org9af9468"><span class="section-number-4">2.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-org7e10529" class="outline-4">
<h4 id="org7e10529"><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-org2e823bc" class="outline-5">
<h5 id="org2e823bc"><span class="section-number-5">2.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org0d88176" class="outline-5">
<h5 id="org0d88176"><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-org366cb7a" class="outline-5">
<h5 id="org366cb7a"><span class="section-number-5">2.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-orgaf064f0" class="outline-5">
<h5 id="orgaf064f0"><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-org006858c" class="outline-4">
<h4 id="org006858c"><span class="section-number-4">2.1.8</span> Compute the energy</h4>
<div id="outline-container-org43b2563" class="outline-4">
<h4 id="org43b2563"><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-orgdb059f1" class="outline-4">
<h4 id="orgdb059f1"><span class="section-number-4">2.1.9</span> Terminate</h4>
<div id="outline-container-org0180ebc" class="outline-4">
<h4 id="org0180ebc"><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-org788ae8f" class="outline-3">
<h3 id="org788ae8f"><span class="section-number-3">2.2</span> Python</h3>
<div id="outline-container-org9335654" class="outline-3">
<h3 id="org9335654"><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-org839c315" class="outline-4">
<h4 id="org839c315"><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-orgd61911c" class="outline-4">
<h4 id="orgd61911c"><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-org617c079" class="outline-4">
<h4 id="org617c079"><span class="section-number-4">2.2.2</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org0e4ba0b" class="outline-4">
<h4 id="org0e4ba0b"><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-org0bfcf25" class="outline-4">
<h4 id="org0bfcf25"><span class="section-number-4">2.2.3</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org080ee21" class="outline-4">
<h4 id="org080ee21"><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-org3e8c412" class="outline-4">
<h4 id="org3e8c412"><span class="section-number-4">2.2.4</span> Read one-electron quantities</h4>
<div id="outline-container-org9b99901" class="outline-4">
<h4 id="org9b99901"><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-org53dee91" class="outline-4">
<h4 id="org53dee91"><span class="section-number-4">2.2.5</span> Read two-electron quantities</h4>
<div id="outline-container-org9fd1bf4" class="outline-4">
<h4 id="org9fd1bf4"><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-orgfacc0aa" class="outline-5">
<h5 id="orgfacc0aa"><span class="section-number-5">2.2.5.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org76cfe1b" class="outline-5">
<h5 id="org76cfe1b"><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-orgac750a9" class="outline-5">
<h5 id="orgac750a9"><span class="section-number-5">2.2.5.2</span> Reduced density matrix</h5>
<div id="outline-container-org7681f76" class="outline-5">
<h5 id="org7681f76"><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-orgf50ad96" class="outline-4">
<h4 id="orgf50ad96"><span class="section-number-4">2.2.6</span> Compute the energy</h4>
<div id="outline-container-orgd8e797e" class="outline-4">
<h4 id="orgd8e797e"><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-orge8a0de0" class="outline-2">
<h2 id="orge8a0de0"><span class="section-number-2">3</span> Reading determinants</h2>
<div id="outline-container-org6cb4cd7" class="outline-2">
<h2 id="org6cb4cd7"><span class="section-number-2">3</span> Reading determinants</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org2d425c8" class="outline-3">
<h3 id="org2d425c8"><span class="section-number-3">3.1</span> Fortran</h3>
<div id="outline-container-orga91a87f" class="outline-3">
<h3 id="orga91a87f"><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: 2024-03-13 Wed 13:26</p>
<p class="date">Created: 2024-03-15 Fri 12:21</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>
<!-- 2024-03-13 Wed 13:26 -->
<!-- 2024-03-15 Fri 12:21 -->
<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: 2024-03-13 Wed 13:26</p>
<p class="date">Created: 2024-03-15 Fri 12:21</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>
<!-- 2024-03-13 Wed 13:26 -->
<!-- 2024-03-15 Fri 12:21 -->
<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: 2024-03-13 Wed 13:26</p>
<p class="date">Created: 2024-03-15 Fri 12:21</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>
<!-- 2024-03-13 Wed 13:26 -->
<!-- 2024-03-15 Fri 12:21 -->
<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="#org7bd9354">1. Format specification</a>
<li><a href="#orgf35f9d0">1. Format specification</a>
<ul>
<li><a href="#org93335c6">1.1. Organization of the data</a></li>
<li><a href="#org638ac8c">1.2. Data types</a></li>
<li><a href="#orgc83de33">1.1. Organization of the data</a></li>
<li><a href="#org48386bd">1.2. Data types</a></li>
</ul>
</li>
<li><a href="#orgf0ccb9f">2. The TREXIO library</a>
<li><a href="#orgc14b738">2. The TREXIO library</a>
<ul>
<li><a href="#orgb51a29c">2.1. The front-end</a></li>
<li><a href="#orgdb0ab66">2.2. The back-end</a></li>
<li><a href="#orga244c9c">2.3. Supported languages</a></li>
<li><a href="#orgb535a0f">2.4. Source code generation and documentation</a></li>
<li><a href="#org2ca94d3">2.5. Availability</a></li>
<li><a href="#orgdd3513f">2.1. The front-end</a></li>
<li><a href="#org077564d">2.2. The back-end</a></li>
<li><a href="#org652c068">2.3. Supported languages</a></li>
<li><a href="#org30bf25d">2.4. Source code generation and documentation</a></li>
<li><a href="#orga07cc5d">2.5. Availability</a></li>
</ul>
</li>
</ul>
@ -366,8 +366,8 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-org7bd9354" class="outline-2">
<h2 id="org7bd9354"><span class="section-number-2">1</span> Format specification</h2>
<div id="outline-container-orgf35f9d0" class="outline-2">
<h2 id="orgf35f9d0"><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-org93335c6" class="outline-3">
<h3 id="org93335c6"><span class="section-number-3">1.1</span> Organization of the data</h3>
<div id="outline-container-orgc83de33" class="outline-3">
<h3 id="orgc83de33"><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-org638ac8c" class="outline-3">
<h3 id="org638ac8c"><span class="section-number-3">1.2</span> Data types</h3>
<div id="outline-container-org48386bd" class="outline-3">
<h3 id="org48386bd"><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-orgf0ccb9f" class="outline-2">
<h2 id="orgf0ccb9f"><span class="section-number-2">2</span> The TREXIO library</h2>
<div id="outline-container-orgc14b738" class="outline-2">
<h2 id="orgc14b738"><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-orgb51a29c" class="outline-3">
<h3 id="orgb51a29c"><span class="section-number-3">2.1</span> The front-end</h3>
<div id="outline-container-orgdd3513f" class="outline-3">
<h3 id="orgdd3513f"><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-orgdb0ab66" class="outline-3">
<h3 id="orgdb0ab66"><span class="section-number-3">2.2</span> The back-end</h3>
<div id="outline-container-org077564d" class="outline-3">
<h3 id="org077564d"><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-orga244c9c" class="outline-3">
<h3 id="orga244c9c"><span class="section-number-3">2.3</span> Supported languages</h3>
<div id="outline-container-org652c068" class="outline-3">
<h3 id="org652c068"><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-orgb535a0f" class="outline-3">
<h3 id="orgb535a0f"><span class="section-number-3">2.4</span> Source code generation and documentation</h3>
<div id="outline-container-org30bf25d" class="outline-3">
<h3 id="org30bf25d"><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-org2ca94d3" class="outline-3">
<h3 id="org2ca94d3"><span class="section-number-3">2.5</span> Availability</h3>
<div id="outline-container-orga07cc5d" class="outline-3">
<h3 id="orga07cc5d"><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: 2024-03-13 Wed 13:26</p>
<p class="date">Created: 2024-03-15 Fri 12:21</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>
<!-- 2024-03-13 Wed 13:25 -->
<!-- 2024-03-15 Fri 12:21 -->
<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="#orgd02b4a5">1. Template for HDF5 definitions</a></li>
<li><a href="#org7cb8197">2. Template for HDF5 structures</a></li>
<li><a href="#orgeb4bf5b">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org9504e06">4. Template for HDF5 has a group</a></li>
<li><a href="#org1a4b6ca">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orge6499fb">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#orgdb92f01">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org8282400">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org6a63e6b">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org38238ca">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org17adfb9">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org5e6401f">12. Source code for the determinant part</a></li>
<li><a href="#org27c95f0">13. Helper functions</a></li>
<li><a href="#org97905b0">1. Template for HDF5 definitions</a></li>
<li><a href="#org249aaf8">2. Template for HDF5 structures</a></li>
<li><a href="#org156fb75">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org0880f3a">4. Template for HDF5 has a group</a></li>
<li><a href="#orga531ff4">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orgc839cee">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org41083c9">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#orgad9f210">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#orgc5481fd">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org37c7f95">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org27a2e4d">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org4d468a6">12. Source code for the determinant part</a></li>
<li><a href="#org5649acd">13. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-orgd02b4a5" class="outline-2">
<h2 id="orgd02b4a5"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-org97905b0" class="outline-2">
<h2 id="org97905b0"><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-org7cb8197" class="outline-2">
<h2 id="org7cb8197"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-org249aaf8" class="outline-2">
<h2 id="org249aaf8"><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-orgeb4bf5b" class="outline-2">
<h2 id="orgeb4bf5b"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-org156fb75" class="outline-2">
<h2 id="org156fb75"><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-org9504e06" class="outline-2">
<h2 id="org9504e06"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-org0880f3a" class="outline-2">
<h2 id="org0880f3a"><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-org1a4b6ca" class="outline-2">
<h2 id="org1a4b6ca"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-orga531ff4" class="outline-2">
<h2 id="orga531ff4"><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-orge6499fb" class="outline-2">
<h2 id="orge6499fb"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-orgc839cee" class="outline-2">
<h2 id="orgc839cee"><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-orgdb92f01" class="outline-2">
<h2 id="orgdb92f01"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-org41083c9" class="outline-2">
<h2 id="org41083c9"><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-org8282400" class="outline-2">
<h2 id="org8282400"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div id="outline-container-orgad9f210" class="outline-2">
<h2 id="orgad9f210"><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-org6a63e6b" class="outline-2">
<h2 id="org6a63e6b"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-orgc5481fd" class="outline-2">
<h2 id="orgc5481fd"><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-org38238ca" class="outline-2">
<h2 id="org38238ca"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-org37c7f95" class="outline-2">
<h2 id="org37c7f95"><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-org17adfb9" class="outline-2">
<h2 id="org17adfb9"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-org27a2e4d" class="outline-2">
<h2 id="org27a2e4d"><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-org5e6401f" class="outline-2">
<h2 id="org5e6401f"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div id="outline-container-org4d468a6" class="outline-2">
<h2 id="org4d468a6"><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-org27c95f0" class="outline-2">
<h2 id="org27c95f0"><span class="section-number-2">13</span> Helper functions</h2>
<div id="outline-container-org5649acd" class="outline-2">
<h2 id="org5649acd"><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: 2024-03-13 Wed 13:25</p>
<p class="date">Created: 2024-03-15 Fri 12:21</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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<head>
<!-- 2024-03-13 Wed 13:25 -->
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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>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="#org3dafc4e">1. Template for group-related structures in text back end</a></li>
<li><a href="#org9b5f8b4">2. Template for general structure in text back end</a></li>
<li><a href="#orgb937834">3. Initialize function (constant part)</a></li>
<li><a href="#org88ec60e">4. Deinitialize function (templated part)</a></li>
<li><a href="#org969fd97">5. Flush function (templated part)</a></li>
<li><a href="#orgc697714">6. Template for text read a group</a></li>
<li><a href="#orgd4eeec9">7. Template for text has a group</a></li>
<li><a href="#org141e7b7">8. Template for text flush a group</a></li>
<li><a href="#orgff8426e">9. Template for text free memory</a></li>
<li><a href="#orgcc5d4ee">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org39e3a83">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org2015873">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orgccf4c17">13. Template for has/read/write a string attribute</a></li>
<li><a href="#orgeba2b54">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orgf114679">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org52aac6a">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org0b06236">17. Source code for the determinant part</a></li>
<li><a href="#orgc34aceb">1. Template for group-related structures in text back end</a></li>
<li><a href="#orgf3f3c40">2. Template for general structure in text back end</a></li>
<li><a href="#org9f29588">3. Initialize function (constant part)</a></li>
<li><a href="#orgdbaf48a">4. Deinitialize function (templated part)</a></li>
<li><a href="#org241b879">5. Flush function (templated part)</a></li>
<li><a href="#org2550dc5">6. Template for text read a group</a></li>
<li><a href="#orgcfa9722">7. Template for text has a group</a></li>
<li><a href="#org7d45629">8. Template for text flush a group</a></li>
<li><a href="#org06fa078">9. Template for text free memory</a></li>
<li><a href="#org97ede06">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org39bdd7e">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org4fd0c6e">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orgff607aa">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org0d4bc00">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org172be12">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#orgb59297b">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org7c1b053">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-org3dafc4e" class="outline-2">
<h2 id="org3dafc4e"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-orgc34aceb" class="outline-2">
<h2 id="orgc34aceb"><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-org9b5f8b4" class="outline-2">
<h2 id="org9b5f8b4"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-orgf3f3c40" class="outline-2">
<h2 id="orgf3f3c40"><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-orgb937834" class="outline-2">
<h2 id="orgb937834"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-org9f29588" class="outline-2">
<h2 id="org9f29588"><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-org88ec60e" class="outline-2">
<h2 id="org88ec60e"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-orgdbaf48a" class="outline-2">
<h2 id="orgdbaf48a"><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-org969fd97" class="outline-2">
<h2 id="org969fd97"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div id="outline-container-org241b879" class="outline-2">
<h2 id="org241b879"><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-orgc697714" class="outline-2">
<h2 id="orgc697714"><span class="section-number-2">6</span> Template for text read a group</h2>
<div id="outline-container-org2550dc5" class="outline-2">
<h2 id="org2550dc5"><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-orgd4eeec9" class="outline-2">
<h2 id="orgd4eeec9"><span class="section-number-2">7</span> Template for text has a group</h2>
<div id="outline-container-orgcfa9722" class="outline-2">
<h2 id="orgcfa9722"><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-org141e7b7" class="outline-2">
<h2 id="org141e7b7"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div id="outline-container-org7d45629" class="outline-2">
<h2 id="org7d45629"><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-orgff8426e" class="outline-2">
<h2 id="orgff8426e"><span class="section-number-2">9</span> Template for text free memory</h2>
<div id="outline-container-org06fa078" class="outline-2">
<h2 id="org06fa078"><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-orgcc5d4ee" class="outline-2">
<h2 id="orgcc5d4ee"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-org97ede06" class="outline-2">
<h2 id="org97ede06"><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-org39e3a83" class="outline-2">
<h2 id="org39e3a83"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-org39bdd7e" class="outline-2">
<h2 id="org39bdd7e"><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-org2015873" class="outline-2">
<h2 id="org2015873"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-org4fd0c6e" class="outline-2">
<h2 id="org4fd0c6e"><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-orgccf4c17" class="outline-2">
<h2 id="orgccf4c17"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-orgff607aa" class="outline-2">
<h2 id="orgff607aa"><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-orgeba2b54" class="outline-2">
<h2 id="orgeba2b54"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-org0d4bc00" class="outline-2">
<h2 id="org0d4bc00"><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-orgf114679" class="outline-2">
<h2 id="orgf114679"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div id="outline-container-org172be12" class="outline-2">
<h2 id="org172be12"><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-org52aac6a" class="outline-2">
<h2 id="org52aac6a"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-orgb59297b" class="outline-2">
<h2 id="orgb59297b"><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-org0b06236" class="outline-2">
<h2 id="org0b06236"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div id="outline-container-org7c1b053" class="outline-2">
<h2 id="org7c1b053"><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: 2024-03-13 Wed 13:25</p>
<p class="date">Created: 2024-03-15 Fri 12:21</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

248
trex.html
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<head>
<!-- 2024-03-13 Wed 13:25 -->
<!-- 2024-03-15 Fri 12:21 -->
<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="#org1edba75">1. Metadata (metadata group)</a></li>
<li><a href="#org3b89986">2. System</a>
<li><a href="#org8c747e4">1. Metadata (metadata group)</a></li>
<li><a href="#org326f9a7">2. System</a>
<ul>
<li><a href="#org4e1707a">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org0dbb773">2.2. Cell (cell group)</a></li>
<li><a href="#org43973d3">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org87b520d">2.4. Electron (electron group)</a></li>
<li><a href="#orgfd7c1e9">2.5. Ground or excited states (state group)</a></li>
<li><a href="#org5ef52b1">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#orgd14a3bc">2.2. Cell (cell group)</a></li>
<li><a href="#org9a2f6f3">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org10c2a4c">2.4. Electron (electron group)</a></li>
<li><a href="#org3e2a028">2.5. Ground or excited states (state group)</a></li>
</ul>
</li>
<li><a href="#org8fc358f">3. Basis functions</a>
<li><a href="#org24a3eea">3. Basis functions</a>
<ul>
<li><a href="#org3b1a471">3.1. Basis set (basis group)</a>
<li><a href="#org4e30083">3.1. Basis set (basis group)</a>
<ul>
<li><a href="#orge94f753">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#orgd6e0f75">3.1.2. Numerical orbitals</a></li>
<li><a href="#orgaf21f18">3.1.3. Plane waves</a></li>
<li><a href="#orgc4f6bc6">3.1.4. Data definitions</a></li>
<li><a href="#org7bd20bc">3.1.5. Example</a></li>
<li><a href="#org8128440">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#org7fb8616">3.1.2. Numerical orbitals</a></li>
<li><a href="#org10143b4">3.1.3. Plane waves</a></li>
<li><a href="#org5d33a4c">3.1.4. Data definitions</a></li>
<li><a href="#orgffe2388">3.1.5. Example</a></li>
</ul>
</li>
<li><a href="#org818d02e">3.2. Effective core potentials (ecp group)</a>
<li><a href="#org823b204">3.2. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org44395cf">3.2.1. Example</a></li>
<li><a href="#org520b201">3.2.1. Example</a></li>
</ul>
</li>
<li><a href="#org704500b">3.3. Numerical integration grid (grid group)</a></li>
<li><a href="#orgd7ecf55">3.3. Numerical integration grid (grid group)</a></li>
</ul>
</li>
<li><a href="#orgbda7c9a">4. Orbitals</a>
<li><a href="#org53186a5">4. Orbitals</a>
<ul>
<li><a href="#org65d637b">4.1. Atomic orbitals (ao group)</a>
<li><a href="#orgb2a96ac">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="#org88f32c1">4.2. Molecular orbitals (mo group)</a>
<li><a href="#org8d546a4">4.2. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org0c8c1d6">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgd02df6d">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org56f7344">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org26e39e1">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org5aadd9e">5. Multi-determinant information</a>
<li><a href="#org404cad8">5. Multi-determinant information</a>
<ul>
<li><a href="#orgca34e52">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#orge928f95">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#org540b583">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org5cdabb4">5.4. Reduced density matrices (rdm group)</a></li>
<li><a href="#org3aad3d1">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org9b4e4ee">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#org0678227">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org2aa7104">5.4. Reduced density matrices (rdm group)</a></li>
</ul>
</li>
<li><a href="#org0c8f2e3">6. Correlation factors</a>
<li><a href="#orgb7dd005">6. Correlation factors</a>
<ul>
<li><a href="#org4320379">6.1. Jastrow factor (jastrow group)</a>
<li><a href="#org088a065">6.1. Jastrow factor (jastrow group)</a>
<ul>
<li><a href="#orgf2d8771">6.1.1. CHAMP</a></li>
<li><a href="#org733f718">6.1.2. Mu</a></li>
<li><a href="#org7886e80">6.1.3. Table of values</a></li>
<li><a href="#orgc352261">6.1.1. CHAMP</a></li>
<li><a href="#org68f75c7">6.1.2. Mu</a></li>
<li><a href="#org57a46ff">6.1.3. Table of values</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org2e3fef3">7. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#org73a7c2f">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-org1edba75" class="outline-2">
<h2 id="org1edba75"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org8c747e4" class="outline-2">
<h2 id="org8c747e4"><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="org4fdfcc5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org91acdf5" 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-org3b89986" class="outline-2">
<h2 id="org3b89986"><span class="section-number-2">2</span> System</h2>
<div id="outline-container-org326f9a7" class="outline-2">
<h2 id="org326f9a7"><span class="section-number-2">2</span> System</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org4e1707a" class="outline-3">
<h3 id="org4e1707a"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
<div id="outline-container-org5ef52b1" class="outline-3">
<h3 id="org5ef52b1"><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="orge719e94" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org89b326b" 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-org0dbb773" class="outline-3">
<h3 id="org0dbb773"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
<div id="outline-container-orgd14a3bc" class="outline-3">
<h3 id="orgd14a3bc"><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="org3527c8f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgfb9a6a5" 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-org43973d3" class="outline-3">
<h3 id="org43973d3"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div id="outline-container-org9a2f6f3" class="outline-3">
<h3 id="org9a2f6f3"><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="org6982719" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org207b463" 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-org87b520d" class="outline-3">
<h3 id="org87b520d"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
<div id="outline-container-org10c2a4c" class="outline-3">
<h3 id="org10c2a4c"><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="orge89e782" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org3e3fea2" 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-orgfd7c1e9" class="outline-3">
<h3 id="orgfd7c1e9"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
<div id="outline-container-org3e2a028" class="outline-3">
<h3 id="org3e2a028"><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="orgd1e5f38" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org957f9da" 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-org8fc358f" class="outline-2">
<h2 id="org8fc358f"><span class="section-number-2">3</span> Basis functions</h2>
<div id="outline-container-org24a3eea" class="outline-2">
<h2 id="org24a3eea"><span class="section-number-2">3</span> Basis functions</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org3b1a471" class="outline-3">
<h3 id="org3b1a471"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
<div id="outline-container-org4e30083" class="outline-3">
<h3 id="org4e30083"><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-orge94f753" class="outline-4">
<h4 id="orge94f753"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
<div id="outline-container-org8128440" class="outline-4">
<h4 id="org8128440"><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-orgd6e0f75" class="outline-4">
<h4 id="orgd6e0f75"><span class="section-number-4">3.1.2</span> Numerical orbitals</h4>
<div id="outline-container-org7fb8616" class="outline-4">
<h4 id="org7fb8616"><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-orgaf21f18" class="outline-4">
<h4 id="orgaf21f18"><span class="section-number-4">3.1.3</span> Plane waves</h4>
<div id="outline-container-org10143b4" class="outline-4">
<h4 id="org10143b4"><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-orgc4f6bc6" class="outline-4">
<h4 id="orgc4f6bc6"><span class="section-number-4">3.1.4</span> Data definitions</h4>
<div id="outline-container-org5d33a4c" class="outline-4">
<h4 id="org5d33a4c"><span class="section-number-4">3.1.4</span> Data definitions</h4>
<div class="outline-text-4" id="text-3-1-4">
<table id="org229e8b4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org58ce463" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1250,8 +1250,8 @@ plane waves.
</div>
</div>
<div id="outline-container-org7bd20bc" class="outline-4">
<h4 id="org7bd20bc"><span class="section-number-4">3.1.5</span> Example</h4>
<div id="outline-container-orgffe2388" class="outline-4">
<h4 id="orgffe2388"><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-org818d02e" class="outline-3">
<h3 id="org818d02e"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
<div id="outline-container-org823b204" class="outline-3">
<h3 id="org823b204"><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="orgb6fba56" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf18c3c0" 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-org44395cf" class="outline-4">
<h4 id="org44395cf"><span class="section-number-4">3.2.1</span> Example</h4>
<div id="outline-container-org520b201" class="outline-4">
<h4 id="org520b201"><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-org704500b" class="outline-3">
<h3 id="org704500b"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
<div id="outline-container-orgd7ecf55" class="outline-3">
<h3 id="orgd7ecf55"><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="orgbcba3cc" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgef32840" 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-orgbda7c9a" class="outline-2">
<h2 id="orgbda7c9a"><span class="section-number-2">4</span> Orbitals</h2>
<div id="outline-container-org53186a5" class="outline-2">
<h2 id="org53186a5"><span class="section-number-2">4</span> Orbitals</h2>
<div class="outline-text-2" id="text-4">
</div>
<div id="outline-container-org65d637b" class="outline-3">
<h3 id="org65d637b"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
<div id="outline-container-orgb2a96ac" class="outline-3">
<h3 id="orgb2a96ac"><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="orgef1b278" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf94929d" 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-org84594b4" class="outline-4">
<div id="outline-container-org3a74ecd" 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="orgfe8be24" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org779b54f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1916,7 +1916,7 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org5cbd7ca" class="outline-4">
<div id="outline-container-org97e30a3" 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="org72831f1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga83c439" 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-org88f32c1" class="outline-3">
<h3 id="org88f32c1"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div id="outline-container-org8d546a4" class="outline-3">
<h3 id="org8d546a4"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div class="outline-text-3" id="text-4-2">
<table id="org4abb734" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5cd926d" 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-org0c8c1d6" class="outline-4">
<h4 id="org0c8c1d6"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
<div id="outline-container-org56f7344" class="outline-4">
<h4 id="org56f7344"><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="orgaea2037" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgbbcca06" 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-orgd02df6d" class="outline-4">
<h4 id="orgd02df6d"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
<div id="outline-container-org26e39e1" class="outline-4">
<h4 id="org26e39e1"><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="orgf71d0db" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org1b17395" 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-org5aadd9e" class="outline-2">
<h2 id="org5aadd9e"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div id="outline-container-org404cad8" class="outline-2">
<h2 id="org404cad8"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div class="outline-text-2" id="text-5">
</div>
<div id="outline-container-orgca34e52" class="outline-3">
<h3 id="orgca34e52"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
<div id="outline-container-org3aad3d1" class="outline-3">
<h3 id="org3aad3d1"><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="org8bd1962" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf41221f" 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-orge928f95" class="outline-3">
<h3 id="orge928f95"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
<div id="outline-container-org9b4e4ee" class="outline-3">
<h3 id="org9b4e4ee"><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="orgbacd28c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org76fb8a0" 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-org540b583" class="outline-3">
<h3 id="org540b583"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
<div id="outline-container-org0678227" class="outline-3">
<h3 id="org0678227"><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="org1744cea" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgeabfcc0" 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-org5cdabb4" class="outline-3">
<h3 id="org5cdabb4"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
<div id="outline-container-org2aa7104" class="outline-3">
<h3 id="org2aa7104"><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="org0b7a863" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgdb5af5b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2815,12 +2815,12 @@ expressed in a basis of a one-electron function
</div>
</div>
<div id="outline-container-org0c8f2e3" class="outline-2">
<h2 id="org0c8f2e3"><span class="section-number-2">6</span> Correlation factors</h2>
<div id="outline-container-orgb7dd005" class="outline-2">
<h2 id="orgb7dd005"><span class="section-number-2">6</span> Correlation factors</h2>
<div class="outline-text-2" id="text-6">
</div>
<div id="outline-container-org4320379" class="outline-3">
<h3 id="org4320379"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
<div id="outline-container-org088a065" class="outline-3">
<h3 id="org088a065"><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
@ -2845,8 +2845,8 @@ following:
</ul>
</div>
<div id="outline-container-orgf2d8771" class="outline-4">
<h4 id="orgf2d8771"><span class="section-number-4">6.1.1</span> CHAMP</h4>
<div id="outline-container-orgc352261" class="outline-4">
<h4 id="orgc352261"><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
@ -2947,8 +2947,8 @@ The terms \(J_{\text{ee},ij}^\infty\) and \(J_{\text{eN}}^\infty\) are shifts to
</div>
<div id="outline-container-org733f718" class="outline-4">
<h4 id="org733f718"><span class="section-number-4">6.1.2</span> Mu</h4>
<div id="outline-container-org68f75c7" class="outline-4">
<h4 id="org68f75c7"><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
@ -3045,10 +3045,10 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
</div>
</div>
<div id="outline-container-org7886e80" class="outline-4">
<h4 id="org7886e80"><span class="section-number-4">6.1.3</span> Table of values</h4>
<div id="outline-container-org57a46ff" class="outline-4">
<h4 id="org57a46ff"><span class="section-number-4">6.1.3</span> Table of values</h4>
<div class="outline-text-4" id="text-6-1-3">
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@ -3152,8 +3152,8 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
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<h2 id="org2e3fef3"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
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<h2 id="org73a7c2f"><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
@ -3167,7 +3167,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
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@ -3222,7 +3222,7 @@ of $&uarr;$-spin and then all the $&darr;$-spin.
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<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2024-03-13 Wed 13:25</p>
<p class="date">Created: 2024-03-15 Fri 12:21</p>
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