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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>
<!-- 2024-08-17 Sat 16:33 -->
<!-- 2024-08-17 Sat 17:42 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title>
@ -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: 2024-08-17 Sat 16:33</p>
<p class="date">Created: 2024-08-17 Sat 17:42</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>
<!-- 2024-08-17 Sat 16:33 -->
<!-- 2024-08-17 Sat 17:42 -->
<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="#org4e95cb2">1. Writing nuclear coordinates</a>
<li><a href="#org0019c94">1. Writing nuclear coordinates</a>
<ul>
<li><a href="#org432513b">1.1. C</a></li>
<li><a href="#org19551e6">1.2. Python</a></li>
<li><a href="#org8e4a8aa">1.3. Fortran</a></li>
<li><a href="#orgee39f56">1.1. C</a></li>
<li><a href="#org9c95eba">1.2. Python</a></li>
<li><a href="#orgbba1a27">1.3. Fortran</a></li>
</ul>
</li>
<li><a href="#org61a0248">2. Accessing sparse quantities (integrals)</a>
<li><a href="#org4416b3b">2. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#org015edb3">2.1. Fortran</a>
<li><a href="#orgfafd24a">2.1. Fortran</a>
<ul>
<li><a href="#orgc93b1d2">2.1.1. Declare Temporary variables</a></li>
<li><a href="#org2610304">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org0bcb015">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orge7de686">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org57fcef8">2.1.5. Allocate memory</a></li>
<li><a href="#org71674e1">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org878449c">2.1.7. Read two-electron quantities</a>
<li><a href="#org5acc8bd">2.1.1. Declare Temporary variables</a></li>
<li><a href="#orgbdc4d87">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orga44bc0d">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org3b8c763">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orgc5ee073">2.1.5. Allocate memory</a></li>
<li><a href="#org4b6bfec">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org875db6b">2.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#orgd202607">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org377ab08">2.1.7.2. Reduced density matrix</a></li>
<li><a href="#org8942a77">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org3006df2">2.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org917eec0">2.1.8. Compute the energy</a></li>
<li><a href="#orga9aef3f">2.1.9. Terminate</a></li>
<li><a href="#org9cd3ee5">2.1.8. Compute the energy</a></li>
<li><a href="#org9bd19c1">2.1.9. Terminate</a></li>
</ul>
</li>
<li><a href="#org5409440">2.2. Python</a>
<li><a href="#org7e27e7d">2.2. Python</a>
<ul>
<li><a href="#orgfb86582">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org18fe370">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#org4df0869">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#org23b6362">2.2.4. Read one-electron quantities</a></li>
<li><a href="#orga946ca6">2.2.5. Read two-electron quantities</a>
<li><a href="#orgedaf2db">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org1d8d7ae">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#orgf7babb5">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#org817f4a9">2.2.4. Read one-electron quantities</a></li>
<li><a href="#org0dacce3">2.2.5. Read two-electron quantities</a>
<ul>
<li><a href="#orgebcc7b3">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#org6a7843a">2.2.5.2. Reduced density matrix</a></li>
<li><a href="#orgac902ba">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#orgc0df88d">2.2.5.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org4df720a">2.2.6. Compute the energy</a></li>
<li><a href="#org7d914b7">2.2.6. Compute the energy</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgc10860a">3. Reading determinants</a>
<li><a href="#orgaa420b9">3. Reading determinants</a>
<ul>
<li><a href="#org56d6019">3.1. Fortran</a></li>
<li><a href="#orgc403986">3.1. Fortran</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org4e95cb2" class="outline-2">
<h2 id="org4e95cb2"><span class="section-number-2">1</span> Writing nuclear coordinates</h2>
<div id="outline-container-org0019c94" class="outline-2">
<h2 id="org0019c94"><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-org432513b" class="outline-3">
<h3 id="org432513b"><span class="section-number-3">1.1</span> C</h3>
<div id="outline-container-orgee39f56" class="outline-3">
<h3 id="orgee39f56"><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-org19551e6" class="outline-3">
<h3 id="org19551e6"><span class="section-number-3">1.2</span> Python</h3>
<div id="outline-container-org9c95eba" class="outline-3">
<h3 id="org9c95eba"><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-org8e4a8aa" class="outline-3">
<h3 id="org8e4a8aa"><span class="section-number-3">1.3</span> Fortran</h3>
<div id="outline-container-orgbba1a27" class="outline-3">
<h3 id="orgbba1a27"><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-org61a0248" class="outline-2">
<h2 id="org61a0248"><span class="section-number-2">2</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-org4416b3b" class="outline-2">
<h2 id="org4416b3b"><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-org015edb3" class="outline-3">
<h3 id="org015edb3"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-orgfafd24a" class="outline-3">
<h3 id="orgfafd24a"><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-orgc93b1d2" class="outline-4">
<h4 id="orgc93b1d2"><span class="section-number-4">2.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org5acc8bd" class="outline-4">
<h4 id="org5acc8bd"><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-org2610304" class="outline-4">
<h4 id="org2610304"><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-orgbdc4d87" class="outline-4">
<h4 id="orgbdc4d87"><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-org0bcb015" class="outline-4">
<h4 id="org0bcb015"><span class="section-number-4">2.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orga44bc0d" class="outline-4">
<h4 id="orga44bc0d"><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-orge7de686" class="outline-4">
<h4 id="orge7de686"><span class="section-number-4">2.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org3b8c763" class="outline-4">
<h4 id="org3b8c763"><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-org57fcef8" class="outline-4">
<h4 id="org57fcef8"><span class="section-number-4">2.1.5</span> Allocate memory</h4>
<div id="outline-container-orgc5ee073" class="outline-4">
<h4 id="orgc5ee073"><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-org71674e1" class="outline-4">
<h4 id="org71674e1"><span class="section-number-4">2.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org4b6bfec" class="outline-4">
<h4 id="org4b6bfec"><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-org878449c" class="outline-4">
<h4 id="org878449c"><span class="section-number-4">2.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-org875db6b" class="outline-4">
<h4 id="org875db6b"><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-orgd202607" class="outline-5">
<h5 id="orgd202607"><span class="section-number-5">2.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org8942a77" class="outline-5">
<h5 id="org8942a77"><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-org377ab08" class="outline-5">
<h5 id="org377ab08"><span class="section-number-5">2.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org3006df2" class="outline-5">
<h5 id="org3006df2"><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-org917eec0" class="outline-4">
<h4 id="org917eec0"><span class="section-number-4">2.1.8</span> Compute the energy</h4>
<div id="outline-container-org9cd3ee5" class="outline-4">
<h4 id="org9cd3ee5"><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-orga9aef3f" class="outline-4">
<h4 id="orga9aef3f"><span class="section-number-4">2.1.9</span> Terminate</h4>
<div id="outline-container-org9bd19c1" class="outline-4">
<h4 id="org9bd19c1"><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-org5409440" class="outline-3">
<h3 id="org5409440"><span class="section-number-3">2.2</span> Python</h3>
<div id="outline-container-org7e27e7d" class="outline-3">
<h3 id="org7e27e7d"><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-orgfb86582" class="outline-4">
<h4 id="orgfb86582"><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-orgedaf2db" class="outline-4">
<h4 id="orgedaf2db"><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-org18fe370" class="outline-4">
<h4 id="org18fe370"><span class="section-number-4">2.2.2</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org1d8d7ae" class="outline-4">
<h4 id="org1d8d7ae"><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-org4df0869" class="outline-4">
<h4 id="org4df0869"><span class="section-number-4">2.2.3</span> Read the number of molecular orbitals</h4>
<div id="outline-container-orgf7babb5" class="outline-4">
<h4 id="orgf7babb5"><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-org23b6362" class="outline-4">
<h4 id="org23b6362"><span class="section-number-4">2.2.4</span> Read one-electron quantities</h4>
<div id="outline-container-org817f4a9" class="outline-4">
<h4 id="org817f4a9"><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-orga946ca6" class="outline-4">
<h4 id="orga946ca6"><span class="section-number-4">2.2.5</span> Read two-electron quantities</h4>
<div id="outline-container-org0dacce3" class="outline-4">
<h4 id="org0dacce3"><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-orgebcc7b3" class="outline-5">
<h5 id="orgebcc7b3"><span class="section-number-5">2.2.5.1</span> Electron repulsion integrals</h5>
<div id="outline-container-orgac902ba" class="outline-5">
<h5 id="orgac902ba"><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-org6a7843a" class="outline-5">
<h5 id="org6a7843a"><span class="section-number-5">2.2.5.2</span> Reduced density matrix</h5>
<div id="outline-container-orgc0df88d" class="outline-5">
<h5 id="orgc0df88d"><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-org4df720a" class="outline-4">
<h4 id="org4df720a"><span class="section-number-4">2.2.6</span> Compute the energy</h4>
<div id="outline-container-org7d914b7" class="outline-4">
<h4 id="org7d914b7"><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-orgc10860a" class="outline-2">
<h2 id="orgc10860a"><span class="section-number-2">3</span> Reading determinants</h2>
<div id="outline-container-orgaa420b9" class="outline-2">
<h2 id="orgaa420b9"><span class="section-number-2">3</span> Reading determinants</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org56d6019" class="outline-3">
<h3 id="org56d6019"><span class="section-number-3">3.1</span> Fortran</h3>
<div id="outline-container-orgc403986" class="outline-3">
<h3 id="orgc403986"><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: 2024-08-17 Sat 16:33</p>
<p class="date">Created: 2024-08-17 Sat 17:42</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>
<!-- 2024-08-17 Sat 16:33 -->
<!-- 2024-08-17 Sat 17:42 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title>
@ -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: 2024-08-17 Sat 16:33</p>
<p class="date">Created: 2024-08-17 Sat 17:42</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>
<!-- 2024-08-17 Sat 16:33 -->
<!-- 2024-08-17 Sat 17:42 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Motivation</title>
@ -384,7 +384,7 @@ still lacking, and the purpose of the TREXIO library is to fill this gap.
</div>
<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2024-08-17 Sat 16:33</p>
<p class="date">Created: 2024-08-17 Sat 17:42</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

58
lib.html
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@ -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>
<!-- 2024-08-17 Sat 16:33 -->
<!-- 2024-08-17 Sat 17:42 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>The TREXIO library</title>
@ -346,19 +346,19 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org1a7700d">1. Format specification</a>
<li><a href="#orgb73bfb5">1. Format specification</a>
<ul>
<li><a href="#org6e33766">1.1. Organization of the data</a></li>
<li><a href="#orgbd1d241">1.2. Data types</a></li>
<li><a href="#org31a55ec">1.1. Organization of the data</a></li>
<li><a href="#org7c2b4fc">1.2. Data types</a></li>
</ul>
</li>
<li><a href="#org4d1304d">2. The TREXIO library</a>
<li><a href="#org2a0bd4c">2. The TREXIO library</a>
<ul>
<li><a href="#orgccf6b40">2.1. The front-end</a></li>
<li><a href="#orgf06b2a8">2.2. The back-end</a></li>
<li><a href="#org468742b">2.3. Supported languages</a></li>
<li><a href="#orgc9ab03c">2.4. Source code generation and documentation</a></li>
<li><a href="#org64a3aef">2.5. Availability</a></li>
<li><a href="#orge4be56b">2.1. The front-end</a></li>
<li><a href="#org46261ea">2.2. The back-end</a></li>
<li><a href="#orgc098190">2.3. Supported languages</a></li>
<li><a href="#org55df50f">2.4. Source code generation and documentation</a></li>
<li><a href="#orga9f9f3e">2.5. Availability</a></li>
</ul>
</li>
</ul>
@ -366,8 +366,8 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-org1a7700d" class="outline-2">
<h2 id="org1a7700d"><span class="section-number-2">1</span> Format specification</h2>
<div id="outline-container-orgb73bfb5" class="outline-2">
<h2 id="orgb73bfb5"><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-org6e33766" class="outline-3">
<h3 id="org6e33766"><span class="section-number-3">1.1</span> Organization of the data</h3>
<div id="outline-container-org31a55ec" class="outline-3">
<h3 id="org31a55ec"><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-orgbd1d241" class="outline-3">
<h3 id="orgbd1d241"><span class="section-number-3">1.2</span> Data types</h3>
<div id="outline-container-org7c2b4fc" class="outline-3">
<h3 id="org7c2b4fc"><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-org4d1304d" class="outline-2">
<h2 id="org4d1304d"><span class="section-number-2">2</span> The TREXIO library</h2>
<div id="outline-container-org2a0bd4c" class="outline-2">
<h2 id="org2a0bd4c"><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-orgccf6b40" class="outline-3">
<h3 id="orgccf6b40"><span class="section-number-3">2.1</span> The front-end</h3>
<div id="outline-container-orge4be56b" class="outline-3">
<h3 id="orge4be56b"><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-orgf06b2a8" class="outline-3">
<h3 id="orgf06b2a8"><span class="section-number-3">2.2</span> The back-end</h3>
<div id="outline-container-org46261ea" class="outline-3">
<h3 id="org46261ea"><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-org468742b" class="outline-3">
<h3 id="org468742b"><span class="section-number-3">2.3</span> Supported languages</h3>
<div id="outline-container-orgc098190" class="outline-3">
<h3 id="orgc098190"><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-orgc9ab03c" class="outline-3">
<h3 id="orgc9ab03c"><span class="section-number-3">2.4</span> Source code generation and documentation</h3>
<div id="outline-container-org55df50f" class="outline-3">
<h3 id="org55df50f"><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-org64a3aef" class="outline-3">
<h3 id="org64a3aef"><span class="section-number-3">2.5</span> Availability</h3>
<div id="outline-container-orga9f9f3e" class="outline-3">
<h3 id="orga9f9f3e"><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: 2024-08-17 Sat 16:33</p>
<p class="date">Created: 2024-08-17 Sat 17:42</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2024-08-17 Sat 16:33 -->
<!-- 2024-08-17 Sat 17:42 -->
<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="#org0773eaf">1. Template for HDF5 definitions</a></li>
<li><a href="#org1e7d552">2. Template for HDF5 structures</a></li>
<li><a href="#org20baedf">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org85289f7">4. Template for HDF5 has a group</a></li>
<li><a href="#org596f2a3">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orgea1b2fb">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org9113548">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org34b7e79">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org2d3e07e">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org581a13a">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orge3fc258">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#orgc18f4ea">12. Source code for the determinant part</a></li>
<li><a href="#org80f7b42">13. Helper functions</a></li>
<li><a href="#org7498ae8">1. Template for HDF5 definitions</a></li>
<li><a href="#orgdb0ae2e">2. Template for HDF5 structures</a></li>
<li><a href="#org6e0abb9">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orga297acf">4. Template for HDF5 has a group</a></li>
<li><a href="#orge5ca6fa">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org5b5ba3c">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org9e77b04">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org6f9ff21">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#orgbf943cc">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org81e7c8c">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org2260132">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org56f6321">12. Source code for the determinant part</a></li>
<li><a href="#orge187e1e">13. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-org0773eaf" class="outline-2">
<h2 id="org0773eaf"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-org7498ae8" class="outline-2">
<h2 id="org7498ae8"><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-org1e7d552" class="outline-2">
<h2 id="org1e7d552"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-orgdb0ae2e" class="outline-2">
<h2 id="orgdb0ae2e"><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-org20baedf" class="outline-2">
<h2 id="org20baedf"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-org6e0abb9" class="outline-2">
<h2 id="org6e0abb9"><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-org85289f7" class="outline-2">
<h2 id="org85289f7"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-orga297acf" class="outline-2">
<h2 id="orga297acf"><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-org596f2a3" class="outline-2">
<h2 id="org596f2a3"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-orge5ca6fa" class="outline-2">
<h2 id="orge5ca6fa"><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-orgea1b2fb" class="outline-2">
<h2 id="orgea1b2fb"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-org5b5ba3c" class="outline-2">
<h2 id="org5b5ba3c"><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-org9113548" class="outline-2">
<h2 id="org9113548"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-org9e77b04" class="outline-2">
<h2 id="org9e77b04"><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-org34b7e79" class="outline-2">
<h2 id="org34b7e79"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div id="outline-container-org6f9ff21" class="outline-2">
<h2 id="org6f9ff21"><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-org2d3e07e" class="outline-2">
<h2 id="org2d3e07e"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-orgbf943cc" class="outline-2">
<h2 id="orgbf943cc"><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-org581a13a" class="outline-2">
<h2 id="org581a13a"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-org81e7c8c" class="outline-2">
<h2 id="org81e7c8c"><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-orge3fc258" class="outline-2">
<h2 id="orge3fc258"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-org2260132" class="outline-2">
<h2 id="org2260132"><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-orgc18f4ea" class="outline-2">
<h2 id="orgc18f4ea"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div id="outline-container-org56f6321" class="outline-2">
<h2 id="org56f6321"><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-org80f7b42" class="outline-2">
<h2 id="org80f7b42"><span class="section-number-2">13</span> Helper functions</h2>
<div id="outline-container-orge187e1e" class="outline-2">
<h2 id="orge187e1e"><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: 2024-08-17 Sat 16:33</p>
<p class="date">Created: 2024-08-17 Sat 17:42</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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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="#orgc49ff68">1. Template for group-related structures in text back end</a></li>
<li><a href="#orgd92ead9">2. Template for general structure in text back end</a></li>
<li><a href="#org0415bc6">3. Initialize function (constant part)</a></li>
<li><a href="#org27f379f">4. Deinitialize function (templated part)</a></li>
<li><a href="#orgaef62a8">5. Flush function (templated part)</a></li>
<li><a href="#org382f8a8">6. Template for text read a group</a></li>
<li><a href="#org025fa46">7. Template for text has a group</a></li>
<li><a href="#orga49ee24">8. Template for text flush a group</a></li>
<li><a href="#orgf143957">9. Template for text free memory</a></li>
<li><a href="#org4008326">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orgfb55119">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orgb7df5fd">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orgfa43a42">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org73189e0">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org08f4f9f">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#orga8f906c">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#orga112d88">17. Source code for the determinant part</a></li>
<li><a href="#org83cf39c">1. Template for group-related structures in text back end</a></li>
<li><a href="#org7e9e471">2. Template for general structure in text back end</a></li>
<li><a href="#orgbd37d1f">3. Initialize function (constant part)</a></li>
<li><a href="#orgcf61e88">4. Deinitialize function (templated part)</a></li>
<li><a href="#orgf28d0c1">5. Flush function (templated part)</a></li>
<li><a href="#orga6303cf">6. Template for text read a group</a></li>
<li><a href="#org64e85eb">7. Template for text has a group</a></li>
<li><a href="#orge7c53ec">8. Template for text flush a group</a></li>
<li><a href="#orgd11024c">9. Template for text free memory</a></li>
<li><a href="#orgcb12f69">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org3784dde">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orgc93b379">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orgce679c7">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org3b0a385">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org73bd03a">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#orge5bfc3a">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org56cace9">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-orgc49ff68" class="outline-2">
<h2 id="orgc49ff68"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-org83cf39c" class="outline-2">
<h2 id="org83cf39c"><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-orgd92ead9" class="outline-2">
<h2 id="orgd92ead9"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-org7e9e471" class="outline-2">
<h2 id="org7e9e471"><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-org0415bc6" class="outline-2">
<h2 id="org0415bc6"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-orgbd37d1f" class="outline-2">
<h2 id="orgbd37d1f"><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-org27f379f" class="outline-2">
<h2 id="org27f379f"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-orgcf61e88" class="outline-2">
<h2 id="orgcf61e88"><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-orgaef62a8" class="outline-2">
<h2 id="orgaef62a8"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div id="outline-container-orgf28d0c1" class="outline-2">
<h2 id="orgf28d0c1"><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-org382f8a8" class="outline-2">
<h2 id="org382f8a8"><span class="section-number-2">6</span> Template for text read a group</h2>
<div id="outline-container-orga6303cf" class="outline-2">
<h2 id="orga6303cf"><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-org025fa46" class="outline-2">
<h2 id="org025fa46"><span class="section-number-2">7</span> Template for text has a group</h2>
<div id="outline-container-org64e85eb" class="outline-2">
<h2 id="org64e85eb"><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-orga49ee24" class="outline-2">
<h2 id="orga49ee24"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div id="outline-container-orge7c53ec" class="outline-2">
<h2 id="orge7c53ec"><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-orgf143957" class="outline-2">
<h2 id="orgf143957"><span class="section-number-2">9</span> Template for text free memory</h2>
<div id="outline-container-orgd11024c" class="outline-2">
<h2 id="orgd11024c"><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-org4008326" class="outline-2">
<h2 id="org4008326"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-orgcb12f69" class="outline-2">
<h2 id="orgcb12f69"><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-orgfb55119" class="outline-2">
<h2 id="orgfb55119"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-org3784dde" class="outline-2">
<h2 id="org3784dde"><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-orgb7df5fd" class="outline-2">
<h2 id="orgb7df5fd"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-orgc93b379" class="outline-2">
<h2 id="orgc93b379"><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-orgfa43a42" class="outline-2">
<h2 id="orgfa43a42"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-orgce679c7" class="outline-2">
<h2 id="orgce679c7"><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-org73189e0" class="outline-2">
<h2 id="org73189e0"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-org3b0a385" class="outline-2">
<h2 id="org3b0a385"><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-org08f4f9f" class="outline-2">
<h2 id="org08f4f9f"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div id="outline-container-org73bd03a" class="outline-2">
<h2 id="org73bd03a"><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-orga8f906c" class="outline-2">
<h2 id="orga8f906c"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-orge5bfc3a" class="outline-2">
<h2 id="orge5bfc3a"><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-orga112d88" class="outline-2">
<h2 id="orga112d88"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div id="outline-container-org56cace9" class="outline-2">
<h2 id="org56cace9"><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: 2024-08-17 Sat 16:33</p>
<p class="date">Created: 2024-08-17 Sat 17:42</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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<head>
<!-- 2024-08-17 Sat 16:33 -->
<!-- 2024-08-17 Sat 17:42 -->
<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>Data stored in TREXIO</title>
@ -346,72 +346,72 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org264fafe">1. Metadata (metadata group)</a></li>
<li><a href="#org8e21eb6">2. System</a>
<li><a href="#org185bd2d">1. Metadata (metadata group)</a></li>
<li><a href="#org61f251c">2. System</a>
<ul>
<li><a href="#orgaa249dc">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org00f89db">2.2. Cell (cell group)</a></li>
<li><a href="#orgc4f9eee">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org7b218a6">2.4. Electron (electron group)</a></li>
<li><a href="#orgba9b71d">2.5. Ground or excited states (state group)</a></li>
<li><a href="#orgeec0847">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org266f9bb">2.2. Cell (cell group)</a></li>
<li><a href="#org00eb831">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org9e8f719">2.4. Electron (electron group)</a></li>
<li><a href="#org5450c16">2.5. Ground or excited states (state group)</a></li>
</ul>
</li>
<li><a href="#org22fce0d">3. Basis functions</a>
<li><a href="#orgc580d48">3. Basis functions</a>
<ul>
<li><a href="#orgbc14082">3.1. Basis set (basis group)</a>
<li><a href="#org338fcf6">3.1. Basis set (basis group)</a>
<ul>
<li><a href="#org8575c01">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#orgfd234d3">3.1.2. Numerical orbitals</a></li>
<li><a href="#org27c19bd">3.1.3. Plane waves</a></li>
<li><a href="#org4d39bca">3.1.4. Oscillating orbitals</a></li>
<li><a href="#org8225d50">3.1.5. Data definitions</a></li>
<li><a href="#org1c273d2">3.1.6. Example</a></li>
<li><a href="#org2762acf">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#org3f32661">3.1.2. Numerical orbitals</a></li>
<li><a href="#orgb07f210">3.1.3. Plane waves</a></li>
<li><a href="#org62bfebb">3.1.4. Oscillating orbitals</a></li>
<li><a href="#org1cc3094">3.1.5. Data definitions</a></li>
<li><a href="#org8bc7cf1">3.1.6. Example</a></li>
</ul>
</li>
<li><a href="#org8231c1b">3.2. Effective core potentials (ecp group)</a>
<li><a href="#orgabc4502">3.2. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org1ac076c">3.2.1. Example</a></li>
<li><a href="#org74ceb68">3.2.1. Example</a></li>
</ul>
</li>
<li><a href="#org5967393">3.3. Numerical integration grid (grid group)</a></li>
<li><a href="#org16cff74">3.3. Numerical integration grid (grid group)</a></li>
</ul>
</li>
<li><a href="#orgdec9ba4">4. Orbitals</a>
<li><a href="#orga705148">4. Orbitals</a>
<ul>
<li><a href="#org6b78d3a">4.1. Atomic orbitals (ao group)</a>
<li><a href="#org5b2b798">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="#org816a70d">4.2. Molecular orbitals (mo group)</a>
<li><a href="#orgef40e96">4.2. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org15949d0">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org7022b81">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org1651a8d">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orga25513d">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgde5c63c">5. Multi-determinant information</a>
<li><a href="#orgf40e533">5. Multi-determinant information</a>
<ul>
<li><a href="#org3d325e1">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org467ebf7">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#org8a5fc6a">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#orgee50212">5.4. Reduced density matrices (rdm group)</a></li>
<li><a href="#orgdc389b8">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#orgd858b6d">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#orgb23b713">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org8861646">5.4. Reduced density matrices (rdm group)</a></li>
</ul>
</li>
<li><a href="#org1bf024a">6. Correlation factors</a>
<li><a href="#org521ab67">6. Correlation factors</a>
<ul>
<li><a href="#org5647076">6.1. Jastrow factor (jastrow group)</a>
<li><a href="#orge4d0b1e">6.1. Jastrow factor (jastrow group)</a>
<ul>
<li><a href="#org582a363">6.1.1. CHAMP</a></li>
<li><a href="#orgc3c7894">6.1.2. Mu</a></li>
<li><a href="#org8bc01b5">6.1.3. Table of values</a></li>
<li><a href="#org513c8c2">6.1.1. CHAMP</a></li>
<li><a href="#orgd92a1e8">6.1.2. Mu</a></li>
<li><a href="#org5622936">6.1.3. Table of values</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgf32bed3">7. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#org0c2bee6">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-org264fafe" class="outline-2">
<h2 id="org264fafe"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org185bd2d" class="outline-2">
<h2 id="org185bd2d"><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="org773cc86" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgaec4855" 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-org8e21eb6" class="outline-2">
<h2 id="org8e21eb6"><span class="section-number-2">2</span> System</h2>
<div id="outline-container-org61f251c" class="outline-2">
<h2 id="org61f251c"><span class="section-number-2">2</span> System</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-orgaa249dc" class="outline-3">
<h3 id="orgaa249dc"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
<div id="outline-container-orgeec0847" class="outline-3">
<h3 id="orgeec0847"><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="org4b4b839" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org13aa1f4" 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-org00f89db" class="outline-3">
<h3 id="org00f89db"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
<div id="outline-container-org266f9bb" class="outline-3">
<h3 id="org266f9bb"><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="org4f8c90b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org3b5340d" 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-orgc4f9eee" class="outline-3">
<h3 id="orgc4f9eee"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div id="outline-container-org00eb831" class="outline-3">
<h3 id="org00eb831"><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="org82cd825" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga02b6ea" 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-org7b218a6" class="outline-3">
<h3 id="org7b218a6"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
<div id="outline-container-org9e8f719" class="outline-3">
<h3 id="org9e8f719"><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="org27291e3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org0a995ee" 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-orgba9b71d" class="outline-3">
<h3 id="orgba9b71d"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
<div id="outline-container-org5450c16" class="outline-3">
<h3 id="org5450c16"><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="org9b7fa64" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5d0a1be" 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-org22fce0d" class="outline-2">
<h2 id="org22fce0d"><span class="section-number-2">3</span> Basis functions</h2>
<div id="outline-container-orgc580d48" class="outline-2">
<h2 id="orgc580d48"><span class="section-number-2">3</span> Basis functions</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-orgbc14082" class="outline-3">
<h3 id="orgbc14082"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
<div id="outline-container-org338fcf6" class="outline-3">
<h3 id="org338fcf6"><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-org8575c01" class="outline-4">
<h4 id="org8575c01"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
<div id="outline-container-org2762acf" class="outline-4">
<h4 id="org2762acf"><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-orgfd234d3" class="outline-4">
<h4 id="orgfd234d3"><span class="section-number-4">3.1.2</span> Numerical orbitals</h4>
<div id="outline-container-org3f32661" class="outline-4">
<h4 id="org3f32661"><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-org27c19bd" class="outline-4">
<h4 id="org27c19bd"><span class="section-number-4">3.1.3</span> Plane waves</h4>
<div id="outline-container-orgb07f210" class="outline-4">
<h4 id="orgb07f210"><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-org4d39bca" class="outline-4">
<h4 id="org4d39bca"><span class="section-number-4">3.1.4</span> Oscillating orbitals</h4>
<div id="outline-container-org62bfebb" class="outline-4">
<h4 id="org62bfebb"><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-org8225d50" class="outline-4">
<h4 id="org8225d50"><span class="section-number-4">3.1.5</span> Data definitions</h4>
<div id="outline-container-org1cc3094" class="outline-4">
<h4 id="org1cc3094"><span class="section-number-4">3.1.5</span> Data definitions</h4>
<div class="outline-text-4" id="text-3-1-5">
<table id="org789cf08" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org82fa563" 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-org1c273d2" class="outline-4">
<h4 id="org1c273d2"><span class="section-number-4">3.1.6</span> Example</h4>
<div id="outline-container-org8bc7cf1" class="outline-4">
<h4 id="org8bc7cf1"><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-org8231c1b" class="outline-3">
<h3 id="org8231c1b"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
<div id="outline-container-orgabc4502" class="outline-3">
<h3 id="orgabc4502"><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="orgfbc3dad" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgcebc5e3" 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-org1ac076c" class="outline-4">
<h4 id="org1ac076c"><span class="section-number-4">3.2.1</span> Example</h4>
<div id="outline-container-org74ceb68" class="outline-4">
<h4 id="org74ceb68"><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-org5967393" class="outline-3">
<h3 id="org5967393"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
<div id="outline-container-org16cff74" class="outline-3">
<h3 id="org16cff74"><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="orgbb9b45c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2632861" 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-orgdec9ba4" class="outline-2">
<h2 id="orgdec9ba4"><span class="section-number-2">4</span> Orbitals</h2>
<div id="outline-container-orga705148" class="outline-2">
<h2 id="orga705148"><span class="section-number-2">4</span> Orbitals</h2>
<div class="outline-text-2" id="text-4">
</div>
<div id="outline-container-org6b78d3a" class="outline-3">
<h3 id="org6b78d3a"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
<div id="outline-container-org5b2b798" class="outline-3">
<h3 id="org5b2b798"><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
@ -1912,7 +1912,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</p>
<table id="org53ae473" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org7d6db52" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1971,7 +1971,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</table>
</div>
<div id="outline-container-org393d241" class="outline-4">
<div id="outline-container-org938f5bc" 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">
@ -1989,7 +1989,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="orgd16837b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org043d419" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2097,7 +2097,7 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org0df199b" class="outline-4">
<div id="outline-container-org81ccba1" 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>
@ -2123,7 +2123,7 @@ The Cholesky decomposition of the integrals can also be stored:
\]
</p>
<table id="org47cf83d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd4ac118" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2200,10 +2200,10 @@ The Cholesky decomposition of the integrals can also be stored:
</div>
</div>
<div id="outline-container-org816a70d" class="outline-3">
<h3 id="org816a70d"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div id="outline-container-orgef40e96" class="outline-3">
<h3 id="orgef40e96"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div class="outline-text-3" id="text-4-2">
<table id="org94d779a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgac24d68" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2319,8 +2319,8 @@ is the number of spin-orbitals, twice the number of spatial orbitals.
</div>
<div id="outline-container-org15949d0" class="outline-4">
<h4 id="org15949d0"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
<div id="outline-container-org1651a8d" class="outline-4">
<h4 id="org1651a8d"><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
@ -2328,7 +2328,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="orgea831a0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb921fe9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2436,8 +2436,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org7022b81" class="outline-4">
<h4 id="org7022b81"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
<div id="outline-container-orga25513d" class="outline-4">
<h4 id="orga25513d"><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
@ -2445,7 +2445,7 @@ The operators are the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org9fa057d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5d16a6d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2523,12 +2523,12 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-orgde5c63c" class="outline-2">
<h2 id="orgde5c63c"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div id="outline-container-orgf40e533" class="outline-2">
<h2 id="orgf40e533"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div class="outline-text-2" id="text-5">
</div>
<div id="outline-container-org3d325e1" class="outline-3">
<h3 id="org3d325e1"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
<div id="outline-container-orgdc389b8" class="outline-3">
<h3 id="orgdc389b8"><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 \(\Psi\)
@ -2570,7 +2570,7 @@ 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="org0fa695b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd54cc20" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2622,8 +2622,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
</div>
</div>
<div id="outline-container-org467ebf7" class="outline-3">
<h3 id="org467ebf7"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
<div id="outline-container-orgd858b6d" class="outline-3">
<h3 id="orgd858b6d"><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
@ -2645,7 +2645,7 @@ matrix \(\langle D_I | \psi_J \rangle\) needed to project the CSFs in
the basis of Slater determinants.
</p>
<table id="org86aab4d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd54a582" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2697,8 +2697,8 @@ the basis of Slater determinants.
</div>
</div>
<div id="outline-container-org8a5fc6a" class="outline-3">
<h3 id="org8a5fc6a"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
<div id="outline-container-orgb23b713" class="outline-3">
<h3 id="orgb23b713"><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
@ -2769,7 +2769,7 @@ The order of the indices is chosen such that
<li>\(\dots\)</li>
</ul>
<table id="org2b62902" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5724382" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2861,8 +2861,8 @@ The order of the indices is chosen such that
</div>
</div>
<div id="outline-container-orgee50212" class="outline-3">
<h3 id="orgee50212"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
<div id="outline-container-org8861646" class="outline-3">
<h3 id="org8861646"><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
@ -2934,7 +2934,7 @@ 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="orgac91289" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgbf7d22e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -3099,12 +3099,12 @@ expressed in a basis of a one-electron function
</div>
</div>
<div id="outline-container-org1bf024a" class="outline-2">
<h2 id="org1bf024a"><span class="section-number-2">6</span> Correlation factors</h2>
<div id="outline-container-org521ab67" class="outline-2">
<h2 id="org521ab67"><span class="section-number-2">6</span> Correlation factors</h2>
<div class="outline-text-2" id="text-6">
</div>
<div id="outline-container-org5647076" class="outline-3">
<h3 id="org5647076"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
<div id="outline-container-orge4d0b1e" class="outline-3">
<h3 id="orge4d0b1e"><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
@ -3129,8 +3129,8 @@ following:
</ul>
</div>
<div id="outline-container-org582a363" class="outline-4">
<h4 id="org582a363"><span class="section-number-4">6.1.1</span> CHAMP</h4>
<div id="outline-container-org513c8c2" class="outline-4">
<h4 id="org513c8c2"><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
@ -3231,8 +3231,8 @@ The terms \(J_{\text{ee},ij}^\infty\) and \(J_{\text{eN}}^\infty\) are shifts to
</div>
<div id="outline-container-orgc3c7894" class="outline-4">
<h4 id="orgc3c7894"><span class="section-number-4">6.1.2</span> Mu</h4>
<div id="outline-container-orgd92a1e8" class="outline-4">
<h4 id="orgd92a1e8"><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
@ -3329,10 +3329,10 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
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<h4 id="org8bc01b5"><span class="section-number-4">6.1.3</span> Table of values</h4>
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<h4 id="org5622936"><span class="section-number-4">6.1.3</span> Table of values</h4>
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@ -3450,8 +3450,8 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
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<h2 id="orgf32bed3"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
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<h2 id="org0c2bee6"><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
@ -3465,7 +3465,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
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@ -3527,7 +3527,7 @@ 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: 2024-08-17 Sat 16:33</p>
<p class="date">Created: 2024-08-17 Sat 17:42</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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