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README.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2024-11-21 Thu 08:47 -->
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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>
@ -411,7 +411,7 @@ 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: 2024-11-21 Thu 08:47</p>
<p class="date">Created: 2024-12-11 Wed 15:16</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>
<!-- 2024-11-21 Thu 08:47 -->
<!-- 2024-12-11 Wed 15:16 -->
<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="#orgfb4675b">1. Writing nuclear coordinates</a>
<li><a href="#org04ac694">1. Writing nuclear coordinates</a>
<ul>
<li><a href="#org848122d">1.1. C</a></li>
<li><a href="#org2433ad8">1.2. Python</a></li>
<li><a href="#org0143bf7">1.3. Fortran</a></li>
<li><a href="#org8cd366d">1.1. C</a></li>
<li><a href="#org7c60a38">1.2. Python</a></li>
<li><a href="#org12421b1">1.3. Fortran</a></li>
</ul>
</li>
<li><a href="#org2a5bb95">2. Accessing sparse quantities (integrals)</a>
<li><a href="#org02e26b3">2. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#orgaf0d7a9">2.1. Fortran</a>
<li><a href="#orgd105277">2.1. Fortran</a>
<ul>
<li><a href="#org1c4e039">2.1.1. Declare Temporary variables</a></li>
<li><a href="#org10404a3">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org749ce2f">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org368b849">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orgeb8a461">2.1.5. Allocate memory</a></li>
<li><a href="#org964bf3d">2.1.6. Read one-electron quantities</a></li>
<li><a href="#orgd4057f1">2.1.7. Read two-electron quantities</a>
<li><a href="#org0535368">2.1.1. Declare Temporary variables</a></li>
<li><a href="#orgb82d37d">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org13568f0">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org032c955">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org055717e">2.1.5. Allocate memory</a></li>
<li><a href="#org4801048">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org742c78a">2.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org71db9de">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org3ce64c7">2.1.7.2. Reduced density matrix</a></li>
<li><a href="#org469d9e3">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org1fa6c35">2.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#orgb73d59c">2.1.8. Compute the energy</a></li>
<li><a href="#org2239c2f">2.1.9. Terminate</a></li>
<li><a href="#orga0df31a">2.1.8. Compute the energy</a></li>
<li><a href="#orgc45bf58">2.1.9. Terminate</a></li>
</ul>
</li>
<li><a href="#orgb6e548f">2.2. Python</a>
<li><a href="#org3987957">2.2. Python</a>
<ul>
<li><a href="#org75da077">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org12ac986">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#org394d706">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#org1f93442">2.2.4. Read one-electron quantities</a></li>
<li><a href="#org954a563">2.2.5. Read two-electron quantities</a>
<li><a href="#org970897e">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgf971ee3">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#orgf2b8b2b">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#org6f25fb2">2.2.4. Read one-electron quantities</a></li>
<li><a href="#orgc4259d4">2.2.5. Read two-electron quantities</a>
<ul>
<li><a href="#orgdc6194e">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#org2501a5b">2.2.5.2. Reduced density matrix</a></li>
<li><a href="#org3f1c063">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#orga7386a3">2.2.5.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org5cd3f46">2.2.6. Compute the energy</a></li>
<li><a href="#orgd906b6c">2.2.6. Compute the energy</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgc56a4d6">3. Reading determinants</a>
<li><a href="#org8be7554">3. Reading determinants</a>
<ul>
<li><a href="#org9aea64f">3.1. Fortran</a></li>
<li><a href="#org9bd51f9">3.1. Fortran</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-orgfb4675b" class="outline-2">
<h2 id="orgfb4675b"><span class="section-number-2">1</span> Writing nuclear coordinates</h2>
<div id="outline-container-org04ac694" class="outline-2">
<h2 id="org04ac694"><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-org848122d" class="outline-3">
<h3 id="org848122d"><span class="section-number-3">1.1</span> C</h3>
<div id="outline-container-org8cd366d" class="outline-3">
<h3 id="org8cd366d"><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-org2433ad8" class="outline-3">
<h3 id="org2433ad8"><span class="section-number-3">1.2</span> Python</h3>
<div id="outline-container-org7c60a38" class="outline-3">
<h3 id="org7c60a38"><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-org0143bf7" class="outline-3">
<h3 id="org0143bf7"><span class="section-number-3">1.3</span> Fortran</h3>
<div id="outline-container-org12421b1" class="outline-3">
<h3 id="org12421b1"><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-org2a5bb95" class="outline-2">
<h2 id="org2a5bb95"><span class="section-number-2">2</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-org02e26b3" class="outline-2">
<h2 id="org02e26b3"><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-orgaf0d7a9" class="outline-3">
<h3 id="orgaf0d7a9"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-orgd105277" class="outline-3">
<h3 id="orgd105277"><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-org1c4e039" class="outline-4">
<h4 id="org1c4e039"><span class="section-number-4">2.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org0535368" class="outline-4">
<h4 id="org0535368"><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-org10404a3" class="outline-4">
<h4 id="org10404a3"><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-orgb82d37d" class="outline-4">
<h4 id="orgb82d37d"><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-org749ce2f" class="outline-4">
<h4 id="org749ce2f"><span class="section-number-4">2.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org13568f0" class="outline-4">
<h4 id="org13568f0"><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-org368b849" class="outline-4">
<h4 id="org368b849"><span class="section-number-4">2.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org032c955" class="outline-4">
<h4 id="org032c955"><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-orgeb8a461" class="outline-4">
<h4 id="orgeb8a461"><span class="section-number-4">2.1.5</span> Allocate memory</h4>
<div id="outline-container-org055717e" class="outline-4">
<h4 id="org055717e"><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-org964bf3d" class="outline-4">
<h4 id="org964bf3d"><span class="section-number-4">2.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org4801048" class="outline-4">
<h4 id="org4801048"><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-orgd4057f1" class="outline-4">
<h4 id="orgd4057f1"><span class="section-number-4">2.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-org742c78a" class="outline-4">
<h4 id="org742c78a"><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-org71db9de" class="outline-5">
<h5 id="org71db9de"><span class="section-number-5">2.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org469d9e3" class="outline-5">
<h5 id="org469d9e3"><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-org3ce64c7" class="outline-5">
<h5 id="org3ce64c7"><span class="section-number-5">2.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org1fa6c35" class="outline-5">
<h5 id="org1fa6c35"><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-orgb73d59c" class="outline-4">
<h4 id="orgb73d59c"><span class="section-number-4">2.1.8</span> Compute the energy</h4>
<div id="outline-container-orga0df31a" class="outline-4">
<h4 id="orga0df31a"><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-org2239c2f" class="outline-4">
<h4 id="org2239c2f"><span class="section-number-4">2.1.9</span> Terminate</h4>
<div id="outline-container-orgc45bf58" class="outline-4">
<h4 id="orgc45bf58"><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-orgb6e548f" class="outline-3">
<h3 id="orgb6e548f"><span class="section-number-3">2.2</span> Python</h3>
<div id="outline-container-org3987957" class="outline-3">
<h3 id="org3987957"><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-org75da077" class="outline-4">
<h4 id="org75da077"><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-org970897e" class="outline-4">
<h4 id="org970897e"><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-org12ac986" class="outline-4">
<h4 id="org12ac986"><span class="section-number-4">2.2.2</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orgf971ee3" class="outline-4">
<h4 id="orgf971ee3"><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-org394d706" class="outline-4">
<h4 id="org394d706"><span class="section-number-4">2.2.3</span> Read the number of molecular orbitals</h4>
<div id="outline-container-orgf2b8b2b" class="outline-4">
<h4 id="orgf2b8b2b"><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-org1f93442" class="outline-4">
<h4 id="org1f93442"><span class="section-number-4">2.2.4</span> Read one-electron quantities</h4>
<div id="outline-container-org6f25fb2" class="outline-4">
<h4 id="org6f25fb2"><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-org954a563" class="outline-4">
<h4 id="org954a563"><span class="section-number-4">2.2.5</span> Read two-electron quantities</h4>
<div id="outline-container-orgc4259d4" class="outline-4">
<h4 id="orgc4259d4"><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-orgdc6194e" class="outline-5">
<h5 id="orgdc6194e"><span class="section-number-5">2.2.5.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org3f1c063" class="outline-5">
<h5 id="org3f1c063"><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):
@ -1021,8 +1021,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org2501a5b" class="outline-5">
<h5 id="org2501a5b"><span class="section-number-5">2.2.5.2</span> Reduced density matrix</h5>
<div id="outline-container-orga7386a3" class="outline-5">
<h5 id="orga7386a3"><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):
@ -1045,8 +1045,8 @@ One needs to read from the TREXIO file:
</div>
</div>
<div id="outline-container-org5cd3f46" class="outline-4">
<h4 id="org5cd3f46"><span class="section-number-4">2.2.6</span> Compute the energy</h4>
<div id="outline-container-orgd906b6c" class="outline-4">
<h4 id="orgd906b6c"><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
@ -1075,12 +1075,12 @@ E &=& E_{\text{NN}} + \sum_{ij} \gamma_{ij}\, \langle j | h | i \rangle\,
</div>
</div>
<div id="outline-container-orgc56a4d6" class="outline-2">
<h2 id="orgc56a4d6"><span class="section-number-2">3</span> Reading determinants</h2>
<div id="outline-container-org8be7554" class="outline-2">
<h2 id="org8be7554"><span class="section-number-2">3</span> Reading determinants</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org9aea64f" class="outline-3">
<h3 id="org9aea64f"><span class="section-number-3">3.1</span> Fortran</h3>
<div id="outline-container-org9bd51f9" class="outline-3">
<h3 id="org9bd51f9"><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>
@ -1159,7 +1159,7 @@ end
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2024-11-21 Thu 08:47</p>
<p class="date">Created: 2024-12-11 Wed 15:16</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>
<!-- 2024-11-21 Thu 08:47 -->
<!-- 2024-12-11 Wed 15:16 -->
<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>
@ -411,7 +411,7 @@ 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: 2024-11-21 Thu 08:47</p>
<p class="date">Created: 2024-12-11 Wed 15:16</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>
<!-- 2024-11-21 Thu 08:47 -->
<!-- 2024-12-11 Wed 15:16 -->
<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: 2024-11-21 Thu 08:47</p>
<p class="date">Created: 2024-12-11 Wed 15:16</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>
<!-- 2024-11-21 Thu 08:47 -->
<!-- 2024-12-11 Wed 15:16 -->
<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="#org291a2bc">1. Format specification</a>
<li><a href="#org37c6e75">1. Format specification</a>
<ul>
<li><a href="#org88cd259">1.1. Organization of the data</a></li>
<li><a href="#org532726a">1.2. Data types</a></li>
<li><a href="#org0361304">1.1. Organization of the data</a></li>
<li><a href="#org1601cbc">1.2. Data types</a></li>
</ul>
</li>
<li><a href="#orga94c654">2. The TREXIO library</a>
<li><a href="#orgc48ad18">2. The TREXIO library</a>
<ul>
<li><a href="#orgf3757e9">2.1. The front-end</a></li>
<li><a href="#org79ce7d2">2.2. The back-end</a></li>
<li><a href="#orga6fd334">2.3. Supported languages</a></li>
<li><a href="#orgfb6b021">2.4. Source code generation and documentation</a></li>
<li><a href="#orgbfa375c">2.5. Availability</a></li>
<li><a href="#org3419488">2.1. The front-end</a></li>
<li><a href="#org5338807">2.2. The back-end</a></li>
<li><a href="#org016cd53">2.3. Supported languages</a></li>
<li><a href="#org92dbb9a">2.4. Source code generation and documentation</a></li>
<li><a href="#org87f4eba">2.5. Availability</a></li>
</ul>
</li>
</ul>
@ -366,8 +366,8 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-org291a2bc" class="outline-2">
<h2 id="org291a2bc"><span class="section-number-2">1</span> Format specification</h2>
<div id="outline-container-org37c6e75" class="outline-2">
<h2 id="org37c6e75"><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-org88cd259" class="outline-3">
<h3 id="org88cd259"><span class="section-number-3">1.1</span> Organization of the data</h3>
<div id="outline-container-org0361304" class="outline-3">
<h3 id="org0361304"><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-org532726a" class="outline-3">
<h3 id="org532726a"><span class="section-number-3">1.2</span> Data types</h3>
<div id="outline-container-org1601cbc" class="outline-3">
<h3 id="org1601cbc"><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-orga94c654" class="outline-2">
<h2 id="orga94c654"><span class="section-number-2">2</span> The TREXIO library</h2>
<div id="outline-container-orgc48ad18" class="outline-2">
<h2 id="orgc48ad18"><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-orgf3757e9" class="outline-3">
<h3 id="orgf3757e9"><span class="section-number-3">2.1</span> The front-end</h3>
<div id="outline-container-org3419488" class="outline-3">
<h3 id="org3419488"><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-org79ce7d2" class="outline-3">
<h3 id="org79ce7d2"><span class="section-number-3">2.2</span> The back-end</h3>
<div id="outline-container-org5338807" class="outline-3">
<h3 id="org5338807"><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-orga6fd334" class="outline-3">
<h3 id="orga6fd334"><span class="section-number-3">2.3</span> Supported languages</h3>
<div id="outline-container-org016cd53" class="outline-3">
<h3 id="org016cd53"><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-orgfb6b021" class="outline-3">
<h3 id="orgfb6b021"><span class="section-number-3">2.4</span> Source code generation and documentation</h3>
<div id="outline-container-org92dbb9a" class="outline-3">
<h3 id="org92dbb9a"><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-orgbfa375c" class="outline-3">
<h3 id="orgbfa375c"><span class="section-number-3">2.5</span> Availability</h3>
<div id="outline-container-org87f4eba" class="outline-3">
<h3 id="org87f4eba"><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: 2024-11-21 Thu 08:47</p>
<p class="date">Created: 2024-12-11 Wed 15:16</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>
<!-- 2024-11-21 Thu 08:47 -->
<!-- 2024-12-11 Wed 15:16 -->
<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="#org0309da4">1. Template for HDF5 definitions</a></li>
<li><a href="#orgeb3e78e">2. Template for HDF5 structures</a></li>
<li><a href="#orgbf2f539">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orge64b782">4. Template for HDF5 has a group</a></li>
<li><a href="#orgbc5b8f0">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org13aab36">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org69a1676">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org8e25d7b">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org38200a9">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org38708da">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orge5aae38">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org7fdd9f6">12. Source code for the determinant part</a></li>
<li><a href="#org329b010">13. Helper functions</a></li>
<li><a href="#orgea8c3fa">1. Template for HDF5 definitions</a></li>
<li><a href="#orgd822a52">2. Template for HDF5 structures</a></li>
<li><a href="#orgc6c7724">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgf864fd6">4. Template for HDF5 has a group</a></li>
<li><a href="#org455adbc">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org5de4f8c">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org9cb03c3">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#orgd650138">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org5e63bce">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org1d9b498">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orgc44ef17">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org6050d81">12. Source code for the determinant part</a></li>
<li><a href="#orgb729760">13. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-org0309da4" class="outline-2">
<h2 id="org0309da4"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-orgea8c3fa" class="outline-2">
<h2 id="orgea8c3fa"><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-orgeb3e78e" class="outline-2">
<h2 id="orgeb3e78e"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-orgd822a52" class="outline-2">
<h2 id="orgd822a52"><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-orgbf2f539" class="outline-2">
<h2 id="orgbf2f539"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-orgc6c7724" class="outline-2">
<h2 id="orgc6c7724"><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-orge64b782" class="outline-2">
<h2 id="orge64b782"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-orgf864fd6" class="outline-2">
<h2 id="orgf864fd6"><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-orgbc5b8f0" class="outline-2">
<h2 id="orgbc5b8f0"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-org455adbc" class="outline-2">
<h2 id="org455adbc"><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-org13aab36" class="outline-2">
<h2 id="org13aab36"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-org5de4f8c" class="outline-2">
<h2 id="org5de4f8c"><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-org69a1676" class="outline-2">
<h2 id="org69a1676"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-org9cb03c3" class="outline-2">
<h2 id="org9cb03c3"><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-org8e25d7b" class="outline-2">
<h2 id="org8e25d7b"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div id="outline-container-orgd650138" class="outline-2">
<h2 id="orgd650138"><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-org38200a9" class="outline-2">
<h2 id="org38200a9"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-org5e63bce" class="outline-2">
<h2 id="org5e63bce"><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-org38708da" class="outline-2">
<h2 id="org38708da"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-org1d9b498" class="outline-2">
<h2 id="org1d9b498"><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-orge5aae38" class="outline-2">
<h2 id="orge5aae38"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-orgc44ef17" class="outline-2">
<h2 id="orgc44ef17"><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-org7fdd9f6" class="outline-2">
<h2 id="org7fdd9f6"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div id="outline-container-org6050d81" class="outline-2">
<h2 id="org6050d81"><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-org329b010" class="outline-2">
<h2 id="org329b010"><span class="section-number-2">13</span> Helper functions</h2>
<div id="outline-container-orgb729760" class="outline-2">
<h2 id="orgb729760"><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: 2024-11-21 Thu 08:47</p>
<p class="date">Created: 2024-12-11 Wed 15:16</p>
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<title>TEXT back end</title>
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<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org6970e60">1. Template for group-related structures in text back end</a></li>
<li><a href="#orgc931d91">2. Template for general structure in text back end</a></li>
<li><a href="#orgdff3ba2">3. Initialize function (constant part)</a></li>
<li><a href="#org48c52b4">4. Deinitialize function (templated part)</a></li>
<li><a href="#orgb03ca75">5. Flush function (templated part)</a></li>
<li><a href="#org2820fe3">6. Template for text read a group</a></li>
<li><a href="#org04b2b72">7. Template for text has a group</a></li>
<li><a href="#orgba9ddac">8. Template for text flush a group</a></li>
<li><a href="#org1b84f9f">9. Template for text free memory</a></li>
<li><a href="#org1546e01">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orgb22d019">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orgd05c745">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org1870409">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org67da71e">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org751fe07">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org3ef4f96">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org8094c6f">17. Source code for the determinant part</a></li>
<li><a href="#org2051d3c">1. Template for group-related structures in text back end</a></li>
<li><a href="#orgddd5ad7">2. Template for general structure in text back end</a></li>
<li><a href="#org86f55f6">3. Initialize function (constant part)</a></li>
<li><a href="#orgfaae870">4. Deinitialize function (templated part)</a></li>
<li><a href="#org3cc97f9">5. Flush function (templated part)</a></li>
<li><a href="#org814bf33">6. Template for text read a group</a></li>
<li><a href="#org6c56f82">7. Template for text has a group</a></li>
<li><a href="#org7aeab30">8. Template for text flush a group</a></li>
<li><a href="#orgb35aafd">9. Template for text free memory</a></li>
<li><a href="#org6ab5a36">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org4e9d542">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org728f8c7">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orgc6d682a">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org735ef81">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orge34f3b0">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org217fcaf">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#orgd9b6d66">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-org6970e60" class="outline-2">
<h2 id="org6970e60"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-org2051d3c" class="outline-2">
<h2 id="org2051d3c"><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-orgc931d91" class="outline-2">
<h2 id="orgc931d91"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-orgddd5ad7" class="outline-2">
<h2 id="orgddd5ad7"><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-orgdff3ba2" class="outline-2">
<h2 id="orgdff3ba2"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-org86f55f6" class="outline-2">
<h2 id="org86f55f6"><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-org48c52b4" class="outline-2">
<h2 id="org48c52b4"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-orgfaae870" class="outline-2">
<h2 id="orgfaae870"><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-orgb03ca75" class="outline-2">
<h2 id="orgb03ca75"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div id="outline-container-org3cc97f9" class="outline-2">
<h2 id="org3cc97f9"><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-org2820fe3" class="outline-2">
<h2 id="org2820fe3"><span class="section-number-2">6</span> Template for text read a group</h2>
<div id="outline-container-org814bf33" class="outline-2">
<h2 id="org814bf33"><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>
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<h2 id="org04b2b72"><span class="section-number-2">7</span> Template for text has a group</h2>
<div id="outline-container-org6c56f82" class="outline-2">
<h2 id="org6c56f82"><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-orgba9ddac" class="outline-2">
<h2 id="orgba9ddac"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div id="outline-container-org7aeab30" class="outline-2">
<h2 id="org7aeab30"><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-org1b84f9f" class="outline-2">
<h2 id="org1b84f9f"><span class="section-number-2">9</span> Template for text free memory</h2>
<div id="outline-container-orgb35aafd" class="outline-2">
<h2 id="orgb35aafd"><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-org1546e01" class="outline-2">
<h2 id="org1546e01"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-org6ab5a36" class="outline-2">
<h2 id="org6ab5a36"><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-orgb22d019" class="outline-2">
<h2 id="orgb22d019"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-org4e9d542" class="outline-2">
<h2 id="org4e9d542"><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-orgd05c745" class="outline-2">
<h2 id="orgd05c745"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-org728f8c7" class="outline-2">
<h2 id="org728f8c7"><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-org1870409" class="outline-2">
<h2 id="org1870409"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-orgc6d682a" class="outline-2">
<h2 id="orgc6d682a"><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-org67da71e" class="outline-2">
<h2 id="org67da71e"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-org735ef81" class="outline-2">
<h2 id="org735ef81"><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-org751fe07" class="outline-2">
<h2 id="org751fe07"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div id="outline-container-orge34f3b0" class="outline-2">
<h2 id="orge34f3b0"><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-org3ef4f96" class="outline-2">
<h2 id="org3ef4f96"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-org217fcaf" class="outline-2">
<h2 id="org217fcaf"><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-org8094c6f" class="outline-2">
<h2 id="org8094c6f"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div id="outline-container-orgd9b6d66" class="outline-2">
<h2 id="orgd9b6d66"><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: 2024-11-21 Thu 08:47</p>
<p class="date">Created: 2024-12-11 Wed 15:16</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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<head>
<!-- 2024-11-21 Thu 08:47 -->
<!-- 2024-12-11 Wed 15:16 -->
<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>
@ -346,72 +346,72 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org9d052f8">1. Metadata (metadata group)</a></li>
<li><a href="#org3778376">2. System</a>
<li><a href="#orgc15d695">1. Metadata (metadata group)</a></li>
<li><a href="#org7107c62">2. System</a>
<ul>
<li><a href="#org6c51e34">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org9befda3">2.2. Cell (cell group)</a></li>
<li><a href="#org8ca40ea">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#orgb44fe1f">2.4. Electron (electron group)</a></li>
<li><a href="#orgee10801">2.5. Ground or excited states (state group)</a></li>
<li><a href="#org8319325">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org74bc4d9">2.2. Cell (cell group)</a></li>
<li><a href="#org7b0dfc6">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org2a18305">2.4. Electron (electron group)</a></li>
<li><a href="#org547dd8f">2.5. Ground or excited states (state group)</a></li>
</ul>
</li>
<li><a href="#org0c49b20">3. Basis functions</a>
<li><a href="#orgf27bdc1">3. Basis functions</a>
<ul>
<li><a href="#org0caa5ec">3.1. Basis set (basis group)</a>
<li><a href="#org813ceed">3.1. Basis set (basis group)</a>
<ul>
<li><a href="#orgba3a857">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#orgdd3fa54">3.1.2. Numerical orbitals</a></li>
<li><a href="#org3c8681b">3.1.3. Plane waves</a></li>
<li><a href="#org59e700d">3.1.4. Oscillating orbitals</a></li>
<li><a href="#orgf2f3c40">3.1.5. Data definitions</a></li>
<li><a href="#org2cdda89">3.1.6. Example</a></li>
<li><a href="#orgddb7ba2">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#orgb91c084">3.1.2. Numerical orbitals</a></li>
<li><a href="#org5cbdf32">3.1.3. Plane waves</a></li>
<li><a href="#org7ad8260">3.1.4. Oscillating orbitals</a></li>
<li><a href="#orgbc361cb">3.1.5. Data definitions</a></li>
<li><a href="#org5eb1f42">3.1.6. Example</a></li>
</ul>
</li>
<li><a href="#orgb06fa76">3.2. Effective core potentials (ecp group)</a>
<li><a href="#orgbd2d955">3.2. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#orgce16a2b">3.2.1. Example</a></li>
<li><a href="#orgb298a45">3.2.1. Example</a></li>
</ul>
</li>
<li><a href="#org8a41f0c">3.3. Numerical integration grid (grid group)</a></li>
<li><a href="#org166d228">3.3. Numerical integration grid (grid group)</a></li>
</ul>
</li>
<li><a href="#org5729ac3">4. Orbitals</a>
<li><a href="#orgddf1ce4">4. Orbitals</a>
<ul>
<li><a href="#orgb328b1e">4.1. Atomic orbitals (ao group)</a>
<li><a href="#org62a7573">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="#orge720cc1">4.2. Molecular orbitals (mo group)</a>
<li><a href="#orgdcb8b3e">4.2. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org818eb93">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org6d0bd96">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org7a9865b">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org26d29b8">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgfbda512">5. Multi-determinant information</a>
<li><a href="#org4ac859e">5. Multi-determinant information</a>
<ul>
<li><a href="#orgc94c7e4">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org08c974a">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#org65245d8">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org46cd5ca">5.4. Reduced density matrices (rdm group)</a></li>
<li><a href="#orgf09dde5">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org55a767a">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#orgc52791f">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org672f562">5.4. Reduced density matrices (rdm group)</a></li>
</ul>
</li>
<li><a href="#org1b3725e">6. Correlation factors</a>
<li><a href="#orgc81532d">6. Correlation factors</a>
<ul>
<li><a href="#org50d3c0a">6.1. Jastrow factor (jastrow group)</a>
<li><a href="#orgb8d876c">6.1. Jastrow factor (jastrow group)</a>
<ul>
<li><a href="#org3bce731">6.1.1. CHAMP</a></li>
<li><a href="#org89e522c">6.1.2. Mu</a></li>
<li><a href="#org834422e">6.1.3. Table of values</a></li>
<li><a href="#orgdd91864">6.1.1. CHAMP</a></li>
<li><a href="#orgfb565ce">6.1.2. Mu</a></li>
<li><a href="#org098463c">6.1.3. Table of values</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgdcc10f3">7. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#org14144bb">7. Quantum Monte Carlo data (qmc group)</a></li>
</ul>
</div>
</div>
@ -433,8 +433,8 @@ contiguous in memory. In the row-major representation, <code>A[i,j]</code> and
<code>A[i,j+1]</code> are contiguous.
</p>
<div id="outline-container-org9d052f8" class="outline-2">
<h2 id="org9d052f8"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-orgc15d695" class="outline-2">
<h2 id="orgc15d695"><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,
@ -444,7 +444,7 @@ have participated to the creation of the file, a list of authors of
the file, and a textual description.
</p>
<table id="orge810aa6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org7874fdb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -537,19 +537,19 @@ value can be manually overwritten (in unsafe mode) from <code>1</code> to <code>
</div>
</div>
<div id="outline-container-org3778376" class="outline-2">
<h2 id="org3778376"><span class="section-number-2">2</span> System</h2>
<div id="outline-container-org7107c62" class="outline-2">
<h2 id="org7107c62"><span class="section-number-2">2</span> System</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org6c51e34" class="outline-3">
<h3 id="org6c51e34"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
<div id="outline-container-org8319325" class="outline-3">
<h3 id="org8319325"><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="org790184c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org0b21f43" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -634,15 +634,15 @@ given in Cartesian \((x,y,z)\) format.
</div>
</div>
<div id="outline-container-org9befda3" class="outline-3">
<h3 id="org9befda3"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
<div id="outline-container-org74bc4d9" class="outline-3">
<h3 id="org74bc4d9"><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="org3a0ca76" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org90ed107" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -726,10 +726,10 @@ used in periodic calculations.
</div>
</div>
<div id="outline-container-org8ca40ea" class="outline-3">
<h3 id="org8ca40ea"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div id="outline-container-org7b0dfc6" class="outline-3">
<h3 id="org7b0dfc6"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div class="outline-text-3" id="text-2-3">
<table id="orge7d089b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgcb90c5c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -789,8 +789,8 @@ used in periodic calculations.
</div>
</div>
<div id="outline-container-orgb44fe1f" class="outline-3">
<h3 id="orgb44fe1f"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
<div id="outline-container-org2a18305" class="outline-3">
<h3 id="org2a18305"><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
@ -809,7 +809,7 @@ the number of &uarr; and &darr; electrons is fixed.
</p>
<table id="org947283c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2b64bec" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -861,8 +861,8 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-orgee10801" class="outline-3">
<h3 id="orgee10801"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
<div id="outline-container-org547dd8f" class="outline-3">
<h3 id="org547dd8f"><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
@ -879,7 +879,7 @@ integrals, etc.
The <code>id</code> and <code>current_label</code> attributes need to be specified for each file.
</p>
<table id="orgc4280db" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5ac1c98" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -956,16 +956,16 @@ The <code>id</code> and <code>current_label</code> attributes need to be specifi
</div>
</div>
<div id="outline-container-org0c49b20" class="outline-2">
<h2 id="org0c49b20"><span class="section-number-2">3</span> Basis functions</h2>
<div id="outline-container-orgf27bdc1" class="outline-2">
<h2 id="orgf27bdc1"><span class="section-number-2">3</span> Basis functions</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org0caa5ec" class="outline-3">
<h3 id="org0caa5ec"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
<div id="outline-container-org813ceed" class="outline-3">
<h3 id="org813ceed"><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-orgba3a857" class="outline-4">
<h4 id="orgba3a857"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
<div id="outline-container-orgddb7ba2" class="outline-4">
<h4 id="orgddb7ba2"><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
@ -1019,8 +1019,8 @@ All the basis set parameters are stored in one-dimensional arrays.
</div>
</div>
<div id="outline-container-orgdd3fa54" class="outline-4">
<h4 id="orgdd3fa54"><span class="section-number-4">3.1.2</span> Numerical orbitals</h4>
<div id="outline-container-orgb91c084" class="outline-4">
<h4 id="orgb91c084"><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
@ -1084,8 +1084,8 @@ reimplement them with consideration for its specific needs.
</div>
</div>
<div id="outline-container-org3c8681b" class="outline-4">
<h4 id="org3c8681b"><span class="section-number-4">3.1.3</span> Plane waves</h4>
<div id="outline-container-org5cbdf32" class="outline-4">
<h4 id="org5cbdf32"><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
@ -1106,8 +1106,8 @@ plane waves.
</div>
</div>
<div id="outline-container-org59e700d" class="outline-4">
<h4 id="org59e700d"><span class="section-number-4">3.1.4</span> Oscillating orbitals</h4>
<div id="outline-container-org7ad8260" class="outline-4">
<h4 id="org7ad8260"><span class="section-number-4">3.1.4</span> Oscillating orbitals</h4>
<div class="outline-text-4" id="text-3-1-4">
<p>
Basis functions can be made oscillating as
@ -1129,10 +1129,10 @@ Oscillation kind can be:
</div>
</div>
<div id="outline-container-orgf2f3c40" class="outline-4">
<h4 id="orgf2f3c40"><span class="section-number-4">3.1.5</span> Data definitions</h4>
<div id="outline-container-orgbc361cb" class="outline-4">
<h4 id="orgbc361cb"><span class="section-number-4">3.1.5</span> Data definitions</h4>
<div class="outline-text-4" id="text-3-1-5">
<table id="org5d5dff0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf47573e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1384,8 +1384,8 @@ Oscillation kind can be:
</div>
</div>
<div id="outline-container-org2cdda89" class="outline-4">
<h4 id="org2cdda89"><span class="section-number-4">3.1.6</span> Example</h4>
<div id="outline-container-org5eb1f42" class="outline-4">
<h4 id="org5eb1f42"><span class="section-number-4">3.1.6</span> Example</h4>
<div class="outline-text-4" id="text-3-1-6">
<p>
For example, consider H<sub>2</sub> with the following basis set (in GAMESS
@ -1463,8 +1463,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-orgb06fa76" class="outline-3">
<h3 id="orgb06fa76"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
<div id="outline-container-orgbd2d955" class="outline-3">
<h3 id="orgbd2d955"><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
@ -1498,7 +1498,7 @@ 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="orgdd0522d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org881d21f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1613,8 +1613,8 @@ If you encounter the aforementioned issue, please report it to our
</p>
</div>
<div id="outline-container-orgce16a2b" class="outline-4">
<h4 id="orgce16a2b"><span class="section-number-4">3.2.1</span> Example</h4>
<div id="outline-container-orgb298a45" class="outline-4">
<h4 id="orgb298a45"><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
@ -1677,8 +1677,8 @@ power = [
</div>
</div>
<div id="outline-container-org8a41f0c" class="outline-3">
<h3 id="org8a41f0c"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
<div id="outline-container-org166d228" class="outline-3">
<h3 id="org166d228"><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
@ -1693,7 +1693,7 @@ 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="org7f665f6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga17247c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1826,12 +1826,12 @@ Feel free to submit a PR if you find missing options/functionalities.
</div>
</div>
<div id="outline-container-org5729ac3" class="outline-2">
<h2 id="org5729ac3"><span class="section-number-2">4</span> Orbitals</h2>
<div id="outline-container-orgddf1ce4" class="outline-2">
<h2 id="orgddf1ce4"><span class="section-number-2">4</span> Orbitals</h2>
<div class="outline-text-2" id="text-4">
</div>
<div id="outline-container-orgb328b1e" class="outline-3">
<h3 id="orgb328b1e"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
<div id="outline-container-org62a7573" class="outline-3">
<h3 id="org62a7573"><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
@ -1918,7 +1918,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</p>
<table id="org6f32b27" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org3ed2594" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1977,7 +1977,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</table>
</div>
<div id="outline-container-org0b706ed" class="outline-4">
<div id="outline-container-org9a40409" 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">
@ -1995,7 +1995,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="org13e9dbd" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org080faae" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2103,7 +2103,7 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org7030a5d" class="outline-4">
<div id="outline-container-orgb29cc5f" 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>
@ -2129,7 +2129,7 @@ The Cholesky decomposition of the integrals can also be stored:
\]
</p>
<table id="org72b1e1c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga3baf96" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2206,10 +2206,10 @@ The Cholesky decomposition of the integrals can also be stored:
</div>
</div>
<div id="outline-container-orge720cc1" class="outline-3">
<h3 id="orge720cc1"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div id="outline-container-orgdcb8b3e" class="outline-3">
<h3 id="orgdcb8b3e"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div class="outline-text-3" id="text-4-2">
<table id="org2b0aeb2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf02b793" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2325,8 +2325,8 @@ is the number of spin-orbitals, twice the number of spatial orbitals.
</div>
<div id="outline-container-org818eb93" class="outline-4">
<h4 id="org818eb93"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
<div id="outline-container-org7a9865b" class="outline-4">
<h4 id="org7a9865b"><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
@ -2334,7 +2334,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="orgc68d589" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org1a9dfb2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2442,8 +2442,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org6d0bd96" class="outline-4">
<h4 id="org6d0bd96"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
<div id="outline-container-org26d29b8" class="outline-4">
<h4 id="org26d29b8"><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
@ -2451,7 +2451,7 @@ The operators are the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="orgd2df203" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org330e972" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2529,12 +2529,12 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-orgfbda512" class="outline-2">
<h2 id="orgfbda512"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div id="outline-container-org4ac859e" class="outline-2">
<h2 id="org4ac859e"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div class="outline-text-2" id="text-5">
</div>
<div id="outline-container-orgc94c7e4" class="outline-3">
<h3 id="orgc94c7e4"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
<div id="outline-container-orgf09dde5" class="outline-3">
<h3 id="orgf09dde5"><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 \(\Psi\)
@ -2576,7 +2576,7 @@ 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="orgf382254" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc647b4a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2628,8 +2628,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
</div>
</div>
<div id="outline-container-org08c974a" class="outline-3">
<h3 id="org08c974a"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
<div id="outline-container-org55a767a" class="outline-3">
<h3 id="org55a767a"><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
@ -2651,7 +2651,7 @@ matrix \(\langle D_I | \psi_J \rangle\) needed to project the CSFs in
the basis of Slater determinants.
</p>
<table id="org83bacee" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org6a17b71" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2703,8 +2703,8 @@ the basis of Slater determinants.
</div>
</div>
<div id="outline-container-org65245d8" class="outline-3">
<h3 id="org65245d8"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
<div id="outline-container-orgc52791f" class="outline-3">
<h3 id="orgc52791f"><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
@ -2775,7 +2775,7 @@ The order of the indices is chosen such that
<li>\(\dots\)</li>
</ul>
<table id="org174e0bc" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org1a8e5e4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2867,8 +2867,8 @@ The order of the indices is chosen such that
</div>
</div>
<div id="outline-container-org46cd5ca" class="outline-3">
<h3 id="org46cd5ca"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
<div id="outline-container-org672f562" class="outline-3">
<h3 id="org672f562"><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
@ -2940,7 +2940,7 @@ 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="org17241bc" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org14baf18" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -3105,12 +3105,12 @@ expressed in a basis of a one-electron function
</div>
</div>
<div id="outline-container-org1b3725e" class="outline-2">
<h2 id="org1b3725e"><span class="section-number-2">6</span> Correlation factors</h2>
<div id="outline-container-orgc81532d" class="outline-2">
<h2 id="orgc81532d"><span class="section-number-2">6</span> Correlation factors</h2>
<div class="outline-text-2" id="text-6">
</div>
<div id="outline-container-org50d3c0a" class="outline-3">
<h3 id="org50d3c0a"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
<div id="outline-container-orgb8d876c" class="outline-3">
<h3 id="orgb8d876c"><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
@ -3135,8 +3135,8 @@ following:
</ul>
</div>
<div id="outline-container-org3bce731" class="outline-4">
<h4 id="org3bce731"><span class="section-number-4">6.1.1</span> CHAMP</h4>
<div id="outline-container-orgdd91864" class="outline-4">
<h4 id="orgdd91864"><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
@ -3237,8 +3237,8 @@ The terms \(J_{\text{ee},ij}^\infty\) and \(J_{\text{eN}}^\infty\) are shifts to
</div>
<div id="outline-container-org89e522c" class="outline-4">
<h4 id="org89e522c"><span class="section-number-4">6.1.2</span> Mu</h4>
<div id="outline-container-orgfb565ce" class="outline-4">
<h4 id="orgfb565ce"><span class="section-number-4">6.1.2</span> Mu</h4>
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<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
@ -3335,10 +3335,10 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
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<h4 id="org834422e"><span class="section-number-4">6.1.3</span> Table of values</h4>
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<h4 id="org098463c"><span class="section-number-4">6.1.3</span> Table of values</h4>
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@ -3456,8 +3456,8 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
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<h2 id="orgdcc10f3"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
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<h2 id="org14144bb"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
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<p>
In quantum Monte Carlo calculations, the wave function is evaluated
@ -3471,7 +3471,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
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@ -3533,7 +3533,7 @@ of $&uarr;$-spin and then all the $&darr;$-spin.
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<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2024-11-21 Thu 08:47</p>
<p class="date">Created: 2024-12-11 Wed 15:16</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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