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README.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2024-08-17 Sat 19:59 -->
<!-- 2024-08-17 Sat 20:27 -->
<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 19:59</p>
<p class="date">Created: 2024-08-17 Sat 20:27</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2024-08-17 Sat 19:59 -->
<!-- 2024-08-17 Sat 20:27 -->
<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="#org4b6ae28">1. Writing nuclear coordinates</a>
<li><a href="#org400fa53">1. Writing nuclear coordinates</a>
<ul>
<li><a href="#org19f765e">1.1. C</a></li>
<li><a href="#orgd6903c9">1.2. Python</a></li>
<li><a href="#org868a7dc">1.3. Fortran</a></li>
<li><a href="#org5228cf2">1.1. C</a></li>
<li><a href="#org4d5beea">1.2. Python</a></li>
<li><a href="#orgbf5ef7b">1.3. Fortran</a></li>
</ul>
</li>
<li><a href="#orgb8e5493">2. Accessing sparse quantities (integrals)</a>
<li><a href="#org8f7c734">2. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#orge55aa33">2.1. Fortran</a>
<li><a href="#org315e428">2.1. Fortran</a>
<ul>
<li><a href="#orgcd3a0aa">2.1.1. Declare Temporary variables</a></li>
<li><a href="#org32ac09f">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org0bdf769">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orga3aa48d">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org3581e2f">2.1.5. Allocate memory</a></li>
<li><a href="#org1f0b623">2.1.6. Read one-electron quantities</a></li>
<li><a href="#orgcf17b4f">2.1.7. Read two-electron quantities</a>
<li><a href="#org561f90c">2.1.1. Declare Temporary variables</a></li>
<li><a href="#orgd7c5d56">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgd67465a">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org4bfab0e">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org920d909">2.1.5. Allocate memory</a></li>
<li><a href="#orgfb4c78b">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org9b26e9c">2.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#orge75e7ca">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org0c56989">2.1.7.2. Reduced density matrix</a></li>
<li><a href="#orge79b211">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#orgbaeb463">2.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org7d54e2a">2.1.8. Compute the energy</a></li>
<li><a href="#orga8cb6a1">2.1.9. Terminate</a></li>
<li><a href="#org73fbe42">2.1.8. Compute the energy</a></li>
<li><a href="#org2805014">2.1.9. Terminate</a></li>
</ul>
</li>
<li><a href="#orge16494d">2.2. Python</a>
<li><a href="#org8574b41">2.2. Python</a>
<ul>
<li><a href="#orgbc2797d">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org92fc830">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#orga2ac4ee">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#orgf88a9ef">2.2.4. Read one-electron quantities</a></li>
<li><a href="#orga22a7a5">2.2.5. Read two-electron quantities</a>
<li><a href="#org2fc482e">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orge5d52d2">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#org0b89865">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#org955fa3b">2.2.4. Read one-electron quantities</a></li>
<li><a href="#orgad8d4e6">2.2.5. Read two-electron quantities</a>
<ul>
<li><a href="#org62af957">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#org218ccbb">2.2.5.2. Reduced density matrix</a></li>
<li><a href="#org3a41c57">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#org3bb2ba9">2.2.5.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org5e14eb0">2.2.6. Compute the energy</a></li>
<li><a href="#orgac2756c">2.2.6. Compute the energy</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orga28c8de">3. Reading determinants</a>
<li><a href="#orga23c9b6">3. Reading determinants</a>
<ul>
<li><a href="#org03f166b">3.1. Fortran</a></li>
<li><a href="#orga89cd5b">3.1. Fortran</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org4b6ae28" class="outline-2">
<h2 id="org4b6ae28"><span class="section-number-2">1</span> Writing nuclear coordinates</h2>
<div id="outline-container-org400fa53" class="outline-2">
<h2 id="org400fa53"><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-org19f765e" class="outline-3">
<h3 id="org19f765e"><span class="section-number-3">1.1</span> C</h3>
<div id="outline-container-org5228cf2" class="outline-3">
<h3 id="org5228cf2"><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-orgd6903c9" class="outline-3">
<h3 id="orgd6903c9"><span class="section-number-3">1.2</span> Python</h3>
<div id="outline-container-org4d5beea" class="outline-3">
<h3 id="org4d5beea"><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-org868a7dc" class="outline-3">
<h3 id="org868a7dc"><span class="section-number-3">1.3</span> Fortran</h3>
<div id="outline-container-orgbf5ef7b" class="outline-3">
<h3 id="orgbf5ef7b"><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-orgb8e5493" class="outline-2">
<h2 id="orgb8e5493"><span class="section-number-2">2</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-org8f7c734" class="outline-2">
<h2 id="org8f7c734"><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-orge55aa33" class="outline-3">
<h3 id="orge55aa33"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-org315e428" class="outline-3">
<h3 id="org315e428"><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-orgcd3a0aa" class="outline-4">
<h4 id="orgcd3a0aa"><span class="section-number-4">2.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org561f90c" class="outline-4">
<h4 id="org561f90c"><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-org32ac09f" class="outline-4">
<h4 id="org32ac09f"><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-orgd7c5d56" class="outline-4">
<h4 id="orgd7c5d56"><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-org0bdf769" class="outline-4">
<h4 id="org0bdf769"><span class="section-number-4">2.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orgd67465a" class="outline-4">
<h4 id="orgd67465a"><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-orga3aa48d" class="outline-4">
<h4 id="orga3aa48d"><span class="section-number-4">2.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org4bfab0e" class="outline-4">
<h4 id="org4bfab0e"><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-org3581e2f" class="outline-4">
<h4 id="org3581e2f"><span class="section-number-4">2.1.5</span> Allocate memory</h4>
<div id="outline-container-org920d909" class="outline-4">
<h4 id="org920d909"><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-org1f0b623" class="outline-4">
<h4 id="org1f0b623"><span class="section-number-4">2.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-orgfb4c78b" class="outline-4">
<h4 id="orgfb4c78b"><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-orgcf17b4f" class="outline-4">
<h4 id="orgcf17b4f"><span class="section-number-4">2.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-org9b26e9c" class="outline-4">
<h4 id="org9b26e9c"><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-orge75e7ca" class="outline-5">
<h5 id="orge75e7ca"><span class="section-number-5">2.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-orge79b211" class="outline-5">
<h5 id="orge79b211"><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-org0c56989" class="outline-5">
<h5 id="org0c56989"><span class="section-number-5">2.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-orgbaeb463" class="outline-5">
<h5 id="orgbaeb463"><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-org7d54e2a" class="outline-4">
<h4 id="org7d54e2a"><span class="section-number-4">2.1.8</span> Compute the energy</h4>
<div id="outline-container-org73fbe42" class="outline-4">
<h4 id="org73fbe42"><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-orga8cb6a1" class="outline-4">
<h4 id="orga8cb6a1"><span class="section-number-4">2.1.9</span> Terminate</h4>
<div id="outline-container-org2805014" class="outline-4">
<h4 id="org2805014"><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-orge16494d" class="outline-3">
<h3 id="orge16494d"><span class="section-number-3">2.2</span> Python</h3>
<div id="outline-container-org8574b41" class="outline-3">
<h3 id="org8574b41"><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-orgbc2797d" class="outline-4">
<h4 id="orgbc2797d"><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-org2fc482e" class="outline-4">
<h4 id="org2fc482e"><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-org92fc830" class="outline-4">
<h4 id="org92fc830"><span class="section-number-4">2.2.2</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orge5d52d2" class="outline-4">
<h4 id="orge5d52d2"><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-orga2ac4ee" class="outline-4">
<h4 id="orga2ac4ee"><span class="section-number-4">2.2.3</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org0b89865" class="outline-4">
<h4 id="org0b89865"><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-orgf88a9ef" class="outline-4">
<h4 id="orgf88a9ef"><span class="section-number-4">2.2.4</span> Read one-electron quantities</h4>
<div id="outline-container-org955fa3b" class="outline-4">
<h4 id="org955fa3b"><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-orga22a7a5" class="outline-4">
<h4 id="orga22a7a5"><span class="section-number-4">2.2.5</span> Read two-electron quantities</h4>
<div id="outline-container-orgad8d4e6" class="outline-4">
<h4 id="orgad8d4e6"><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-org62af957" class="outline-5">
<h5 id="org62af957"><span class="section-number-5">2.2.5.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org3a41c57" class="outline-5">
<h5 id="org3a41c57"><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-org218ccbb" class="outline-5">
<h5 id="org218ccbb"><span class="section-number-5">2.2.5.2</span> Reduced density matrix</h5>
<div id="outline-container-org3bb2ba9" class="outline-5">
<h5 id="org3bb2ba9"><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-org5e14eb0" class="outline-4">
<h4 id="org5e14eb0"><span class="section-number-4">2.2.6</span> Compute the energy</h4>
<div id="outline-container-orgac2756c" class="outline-4">
<h4 id="orgac2756c"><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-orga28c8de" class="outline-2">
<h2 id="orga28c8de"><span class="section-number-2">3</span> Reading determinants</h2>
<div id="outline-container-orga23c9b6" class="outline-2">
<h2 id="orga23c9b6"><span class="section-number-2">3</span> Reading determinants</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org03f166b" class="outline-3">
<h3 id="org03f166b"><span class="section-number-3">3.1</span> Fortran</h3>
<div id="outline-container-orga89cd5b" class="outline-3">
<h3 id="orga89cd5b"><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 19:59</p>
<p class="date">Created: 2024-08-17 Sat 20:27</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 19:59 -->
<!-- 2024-08-17 Sat 20:27 -->
<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 19:59</p>
<p class="date">Created: 2024-08-17 Sat 20:27</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 19:59 -->
<!-- 2024-08-17 Sat 20:27 -->
<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 19:59</p>
<p class="date">Created: 2024-08-17 Sat 20:27</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 19:59 -->
<!-- 2024-08-17 Sat 20:27 -->
<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="#org9447a6d">1. Format specification</a>
<li><a href="#org010934f">1. Format specification</a>
<ul>
<li><a href="#org2f13fb2">1.1. Organization of the data</a></li>
<li><a href="#org0ab7366">1.2. Data types</a></li>
<li><a href="#org43c5340">1.1. Organization of the data</a></li>
<li><a href="#org53b1859">1.2. Data types</a></li>
</ul>
</li>
<li><a href="#orgea3ef09">2. The TREXIO library</a>
<li><a href="#org8673b2a">2. The TREXIO library</a>
<ul>
<li><a href="#org57ec2b3">2.1. The front-end</a></li>
<li><a href="#org72c8719">2.2. The back-end</a></li>
<li><a href="#orgbcd08ae">2.3. Supported languages</a></li>
<li><a href="#org461d82e">2.4. Source code generation and documentation</a></li>
<li><a href="#org798defc">2.5. Availability</a></li>
<li><a href="#org31ae6b0">2.1. The front-end</a></li>
<li><a href="#org2b4502f">2.2. The back-end</a></li>
<li><a href="#org5ca1184">2.3. Supported languages</a></li>
<li><a href="#orgf081a39">2.4. Source code generation and documentation</a></li>
<li><a href="#org87ed0e7">2.5. Availability</a></li>
</ul>
</li>
</ul>
@ -366,8 +366,8 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-org9447a6d" class="outline-2">
<h2 id="org9447a6d"><span class="section-number-2">1</span> Format specification</h2>
<div id="outline-container-org010934f" class="outline-2">
<h2 id="org010934f"><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-org2f13fb2" class="outline-3">
<h3 id="org2f13fb2"><span class="section-number-3">1.1</span> Organization of the data</h3>
<div id="outline-container-org43c5340" class="outline-3">
<h3 id="org43c5340"><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-org0ab7366" class="outline-3">
<h3 id="org0ab7366"><span class="section-number-3">1.2</span> Data types</h3>
<div id="outline-container-org53b1859" class="outline-3">
<h3 id="org53b1859"><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-orgea3ef09" class="outline-2">
<h2 id="orgea3ef09"><span class="section-number-2">2</span> The TREXIO library</h2>
<div id="outline-container-org8673b2a" class="outline-2">
<h2 id="org8673b2a"><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-org57ec2b3" class="outline-3">
<h3 id="org57ec2b3"><span class="section-number-3">2.1</span> The front-end</h3>
<div id="outline-container-org31ae6b0" class="outline-3">
<h3 id="org31ae6b0"><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-org72c8719" class="outline-3">
<h3 id="org72c8719"><span class="section-number-3">2.2</span> The back-end</h3>
<div id="outline-container-org2b4502f" class="outline-3">
<h3 id="org2b4502f"><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-orgbcd08ae" class="outline-3">
<h3 id="orgbcd08ae"><span class="section-number-3">2.3</span> Supported languages</h3>
<div id="outline-container-org5ca1184" class="outline-3">
<h3 id="org5ca1184"><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-org461d82e" class="outline-3">
<h3 id="org461d82e"><span class="section-number-3">2.4</span> Source code generation and documentation</h3>
<div id="outline-container-orgf081a39" class="outline-3">
<h3 id="orgf081a39"><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-org798defc" class="outline-3">
<h3 id="org798defc"><span class="section-number-3">2.5</span> Availability</h3>
<div id="outline-container-org87ed0e7" class="outline-3">
<h3 id="org87ed0e7"><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 19:59</p>
<p class="date">Created: 2024-08-17 Sat 20:27</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 19:59 -->
<!-- 2024-08-17 Sat 20:27 -->
<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="#orge8e292c">1. Template for HDF5 definitions</a></li>
<li><a href="#org5c79c87">2. Template for HDF5 structures</a></li>
<li><a href="#orge33704a">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org4a40653">4. Template for HDF5 has a group</a></li>
<li><a href="#orgc5ed0d5">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orgf9a11f9">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org3c7629e">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#orgf89da6a">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#orgcbaabe4">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org2b1814a">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orgc3f1532">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org0698430">12. Source code for the determinant part</a></li>
<li><a href="#org54043a0">13. Helper functions</a></li>
<li><a href="#org7bd47b7">1. Template for HDF5 definitions</a></li>
<li><a href="#orgfb1b9be">2. Template for HDF5 structures</a></li>
<li><a href="#org6621000">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org4d14a21">4. Template for HDF5 has a group</a></li>
<li><a href="#orgfedc676">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org2aa871b">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org3624c47">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#orgdbc7d08">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#orgf280727">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#orgbb28145">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org259da9f">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#orgbe33074">12. Source code for the determinant part</a></li>
<li><a href="#orgdc6d1bf">13. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-orge8e292c" class="outline-2">
<h2 id="orge8e292c"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-org7bd47b7" class="outline-2">
<h2 id="org7bd47b7"><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-org5c79c87" class="outline-2">
<h2 id="org5c79c87"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-orgfb1b9be" class="outline-2">
<h2 id="orgfb1b9be"><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-orge33704a" class="outline-2">
<h2 id="orge33704a"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-org6621000" class="outline-2">
<h2 id="org6621000"><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-org4a40653" class="outline-2">
<h2 id="org4a40653"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-org4d14a21" class="outline-2">
<h2 id="org4d14a21"><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-orgc5ed0d5" class="outline-2">
<h2 id="orgc5ed0d5"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-orgfedc676" class="outline-2">
<h2 id="orgfedc676"><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-orgf9a11f9" class="outline-2">
<h2 id="orgf9a11f9"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-org2aa871b" class="outline-2">
<h2 id="org2aa871b"><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-org3c7629e" class="outline-2">
<h2 id="org3c7629e"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-org3624c47" class="outline-2">
<h2 id="org3624c47"><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-orgf89da6a" class="outline-2">
<h2 id="orgf89da6a"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div id="outline-container-orgdbc7d08" class="outline-2">
<h2 id="orgdbc7d08"><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-orgcbaabe4" class="outline-2">
<h2 id="orgcbaabe4"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-orgf280727" class="outline-2">
<h2 id="orgf280727"><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-org2b1814a" class="outline-2">
<h2 id="org2b1814a"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-orgbb28145" class="outline-2">
<h2 id="orgbb28145"><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-orgc3f1532" class="outline-2">
<h2 id="orgc3f1532"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-org259da9f" class="outline-2">
<h2 id="org259da9f"><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-org0698430" class="outline-2">
<h2 id="org0698430"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div id="outline-container-orgbe33074" class="outline-2">
<h2 id="orgbe33074"><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-org54043a0" class="outline-2">
<h2 id="org54043a0"><span class="section-number-2">13</span> Helper functions</h2>
<div id="outline-container-orgdc6d1bf" class="outline-2">
<h2 id="orgdc6d1bf"><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 19:59</p>
<p class="date">Created: 2024-08-17 Sat 20:27</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="#orgaaaa387">1. Template for group-related structures in text back end</a></li>
<li><a href="#orgf20a4da">2. Template for general structure in text back end</a></li>
<li><a href="#orgb9c4cb2">3. Initialize function (constant part)</a></li>
<li><a href="#org378df13">4. Deinitialize function (templated part)</a></li>
<li><a href="#org00433c6">5. Flush function (templated part)</a></li>
<li><a href="#orgf1afc10">6. Template for text read a group</a></li>
<li><a href="#org3bba7b0">7. Template for text has a group</a></li>
<li><a href="#orgd9b2aff">8. Template for text flush a group</a></li>
<li><a href="#orge0b818f">9. Template for text free memory</a></li>
<li><a href="#org086cbc1">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org4b2c43d">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org47769d9">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orgefbe8dd">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org3c11bf1">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org6c324f7">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#orgedc5c58">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#orge150315">17. Source code for the determinant part</a></li>
<li><a href="#org6de44b4">1. Template for group-related structures in text back end</a></li>
<li><a href="#org34c4234">2. Template for general structure in text back end</a></li>
<li><a href="#org0cbfd3f">3. Initialize function (constant part)</a></li>
<li><a href="#orgf0cb5e7">4. Deinitialize function (templated part)</a></li>
<li><a href="#org40bd743">5. Flush function (templated part)</a></li>
<li><a href="#orgc0bec9b">6. Template for text read a group</a></li>
<li><a href="#org7531f7f">7. Template for text has a group</a></li>
<li><a href="#org812f6ac">8. Template for text flush a group</a></li>
<li><a href="#orge2182da">9. Template for text free memory</a></li>
<li><a href="#orgb81d257">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org7df2525">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orge9bb095">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orgb948bac">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org72d09e8">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org49dd951">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org703edc9">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org98917af">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-orgaaaa387" class="outline-2">
<h2 id="orgaaaa387"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-org6de44b4" class="outline-2">
<h2 id="org6de44b4"><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-orgf20a4da" class="outline-2">
<h2 id="orgf20a4da"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-org34c4234" class="outline-2">
<h2 id="org34c4234"><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-orgb9c4cb2" class="outline-2">
<h2 id="orgb9c4cb2"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-org0cbfd3f" class="outline-2">
<h2 id="org0cbfd3f"><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-org378df13" class="outline-2">
<h2 id="org378df13"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-orgf0cb5e7" class="outline-2">
<h2 id="orgf0cb5e7"><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-org00433c6" class="outline-2">
<h2 id="org00433c6"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div id="outline-container-org40bd743" class="outline-2">
<h2 id="org40bd743"><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-orgf1afc10" class="outline-2">
<h2 id="orgf1afc10"><span class="section-number-2">6</span> Template for text read a group</h2>
<div id="outline-container-orgc0bec9b" class="outline-2">
<h2 id="orgc0bec9b"><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-org3bba7b0" class="outline-2">
<h2 id="org3bba7b0"><span class="section-number-2">7</span> Template for text has a group</h2>
<div id="outline-container-org7531f7f" class="outline-2">
<h2 id="org7531f7f"><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-orgd9b2aff" class="outline-2">
<h2 id="orgd9b2aff"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div id="outline-container-org812f6ac" class="outline-2">
<h2 id="org812f6ac"><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-orge0b818f" class="outline-2">
<h2 id="orge0b818f"><span class="section-number-2">9</span> Template for text free memory</h2>
<div id="outline-container-orge2182da" class="outline-2">
<h2 id="orge2182da"><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-org086cbc1" class="outline-2">
<h2 id="org086cbc1"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-orgb81d257" class="outline-2">
<h2 id="orgb81d257"><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-org4b2c43d" class="outline-2">
<h2 id="org4b2c43d"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-org7df2525" class="outline-2">
<h2 id="org7df2525"><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-org47769d9" class="outline-2">
<h2 id="org47769d9"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-orge9bb095" class="outline-2">
<h2 id="orge9bb095"><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-orgefbe8dd" class="outline-2">
<h2 id="orgefbe8dd"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-orgb948bac" class="outline-2">
<h2 id="orgb948bac"><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-org3c11bf1" class="outline-2">
<h2 id="org3c11bf1"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-org72d09e8" class="outline-2">
<h2 id="org72d09e8"><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-org6c324f7" class="outline-2">
<h2 id="org6c324f7"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div id="outline-container-org49dd951" class="outline-2">
<h2 id="org49dd951"><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-orgedc5c58" class="outline-2">
<h2 id="orgedc5c58"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-org703edc9" class="outline-2">
<h2 id="org703edc9"><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-orge150315" class="outline-2">
<h2 id="orge150315"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div id="outline-container-org98917af" class="outline-2">
<h2 id="org98917af"><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 19:59</p>
<p class="date">Created: 2024-08-17 Sat 20:27</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 19:59 -->
<!-- 2024-08-17 Sat 20:27 -->
<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="#orgcfd2137">1. Metadata (metadata group)</a></li>
<li><a href="#org043d0b4">2. System</a>
<li><a href="#org9f0180a">1. Metadata (metadata group)</a></li>
<li><a href="#org01feec0">2. System</a>
<ul>
<li><a href="#org711f8cd">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org4e4bb69">2.2. Cell (cell group)</a></li>
<li><a href="#org46248ac">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org59dc3cd">2.4. Electron (electron group)</a></li>
<li><a href="#orgd36050a">2.5. Ground or excited states (state group)</a></li>
<li><a href="#orgf08b0d0">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org823cd3b">2.2. Cell (cell group)</a></li>
<li><a href="#orgcf9b902">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#orgc0e5108">2.4. Electron (electron group)</a></li>
<li><a href="#org5c14721">2.5. Ground or excited states (state group)</a></li>
</ul>
</li>
<li><a href="#org317b02d">3. Basis functions</a>
<li><a href="#org6a5aeca">3. Basis functions</a>
<ul>
<li><a href="#org0c189c6">3.1. Basis set (basis group)</a>
<li><a href="#org822cd5b">3.1. Basis set (basis group)</a>
<ul>
<li><a href="#orgaa542da">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#org0013e89">3.1.2. Numerical orbitals</a></li>
<li><a href="#org037ab4e">3.1.3. Plane waves</a></li>
<li><a href="#org796263a">3.1.4. Oscillating orbitals</a></li>
<li><a href="#orga19073c">3.1.5. Data definitions</a></li>
<li><a href="#org81e846b">3.1.6. Example</a></li>
<li><a href="#org09402b2">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#org8901886">3.1.2. Numerical orbitals</a></li>
<li><a href="#org873597d">3.1.3. Plane waves</a></li>
<li><a href="#org0590568">3.1.4. Oscillating orbitals</a></li>
<li><a href="#org56396c3">3.1.5. Data definitions</a></li>
<li><a href="#orgd5ef5d7">3.1.6. Example</a></li>
</ul>
</li>
<li><a href="#orge5d87a5">3.2. Effective core potentials (ecp group)</a>
<li><a href="#org444ad2c">3.2. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#org071b9ad">3.2.1. Example</a></li>
<li><a href="#orgfc02cd5">3.2.1. Example</a></li>
</ul>
</li>
<li><a href="#org22c4b07">3.3. Numerical integration grid (grid group)</a></li>
<li><a href="#org761b288">3.3. Numerical integration grid (grid group)</a></li>
</ul>
</li>
<li><a href="#orgbab5fbb">4. Orbitals</a>
<li><a href="#org49cdb83">4. Orbitals</a>
<ul>
<li><a href="#org192cc6b">4.1. Atomic orbitals (ao group)</a>
<li><a href="#orge796f49">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="#org157305a">4.2. Molecular orbitals (mo group)</a>
<li><a href="#orga2a9c35">4.2. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org290677a">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orge26029c">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org02a784c">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org5e866ba">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org868a479">5. Multi-determinant information</a>
<li><a href="#orge99a418">5. Multi-determinant information</a>
<ul>
<li><a href="#org2864ce0">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org84986f6">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#org236c150">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#orgcf2e208">5.4. Reduced density matrices (rdm group)</a></li>
<li><a href="#orgd6c2373">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org55c9b57">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#org7d6c586">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#orgbcb3817">5.4. Reduced density matrices (rdm group)</a></li>
</ul>
</li>
<li><a href="#org7dc36b5">6. Correlation factors</a>
<li><a href="#org22d7c18">6. Correlation factors</a>
<ul>
<li><a href="#org4de43c8">6.1. Jastrow factor (jastrow group)</a>
<li><a href="#org432fca4">6.1. Jastrow factor (jastrow group)</a>
<ul>
<li><a href="#orgc9d1855">6.1.1. CHAMP</a></li>
<li><a href="#org163d71f">6.1.2. Mu</a></li>
<li><a href="#org8c75cc0">6.1.3. Table of values</a></li>
<li><a href="#org04b0804">6.1.1. CHAMP</a></li>
<li><a href="#org496e533">6.1.2. Mu</a></li>
<li><a href="#org1ca335f">6.1.3. Table of values</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgff41f26">7. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#org66f0633">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-orgcfd2137" class="outline-2">
<h2 id="orgcfd2137"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org9f0180a" class="outline-2">
<h2 id="org9f0180a"><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="orga711796" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org696983d" 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-org043d0b4" class="outline-2">
<h2 id="org043d0b4"><span class="section-number-2">2</span> System</h2>
<div id="outline-container-org01feec0" class="outline-2">
<h2 id="org01feec0"><span class="section-number-2">2</span> System</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org711f8cd" class="outline-3">
<h3 id="org711f8cd"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
<div id="outline-container-orgf08b0d0" class="outline-3">
<h3 id="orgf08b0d0"><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="org311d3d4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgcc10711" 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-org4e4bb69" class="outline-3">
<h3 id="org4e4bb69"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
<div id="outline-container-org823cd3b" class="outline-3">
<h3 id="org823cd3b"><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="orged4255f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org1c3bbf1" 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-org46248ac" class="outline-3">
<h3 id="org46248ac"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div id="outline-container-orgcf9b902" class="outline-3">
<h3 id="orgcf9b902"><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="org6c3f203" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org47a1a4c" 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-org59dc3cd" class="outline-3">
<h3 id="org59dc3cd"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
<div id="outline-container-orgc0e5108" class="outline-3">
<h3 id="orgc0e5108"><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="org9c4adcd" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org718e52d" 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-orgd36050a" class="outline-3">
<h3 id="orgd36050a"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
<div id="outline-container-org5c14721" class="outline-3">
<h3 id="org5c14721"><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="orgcfa1816" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org8cc4752" 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-org317b02d" class="outline-2">
<h2 id="org317b02d"><span class="section-number-2">3</span> Basis functions</h2>
<div id="outline-container-org6a5aeca" class="outline-2">
<h2 id="org6a5aeca"><span class="section-number-2">3</span> Basis functions</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org0c189c6" class="outline-3">
<h3 id="org0c189c6"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
<div id="outline-container-org822cd5b" class="outline-3">
<h3 id="org822cd5b"><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-orgaa542da" class="outline-4">
<h4 id="orgaa542da"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
<div id="outline-container-org09402b2" class="outline-4">
<h4 id="org09402b2"><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-org0013e89" class="outline-4">
<h4 id="org0013e89"><span class="section-number-4">3.1.2</span> Numerical orbitals</h4>
<div id="outline-container-org8901886" class="outline-4">
<h4 id="org8901886"><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-org037ab4e" class="outline-4">
<h4 id="org037ab4e"><span class="section-number-4">3.1.3</span> Plane waves</h4>
<div id="outline-container-org873597d" class="outline-4">
<h4 id="org873597d"><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-org796263a" class="outline-4">
<h4 id="org796263a"><span class="section-number-4">3.1.4</span> Oscillating orbitals</h4>
<div id="outline-container-org0590568" class="outline-4">
<h4 id="org0590568"><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-orga19073c" class="outline-4">
<h4 id="orga19073c"><span class="section-number-4">3.1.5</span> Data definitions</h4>
<div id="outline-container-org56396c3" class="outline-4">
<h4 id="org56396c3"><span class="section-number-4">3.1.5</span> Data definitions</h4>
<div class="outline-text-4" id="text-3-1-5">
<table id="org85350e6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org7bb236f" 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-org81e846b" class="outline-4">
<h4 id="org81e846b"><span class="section-number-4">3.1.6</span> Example</h4>
<div id="outline-container-orgd5ef5d7" class="outline-4">
<h4 id="orgd5ef5d7"><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-orge5d87a5" class="outline-3">
<h3 id="orge5d87a5"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
<div id="outline-container-org444ad2c" class="outline-3">
<h3 id="org444ad2c"><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="org3f09646" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org34deff2" 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-org071b9ad" class="outline-4">
<h4 id="org071b9ad"><span class="section-number-4">3.2.1</span> Example</h4>
<div id="outline-container-orgfc02cd5" class="outline-4">
<h4 id="orgfc02cd5"><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-org22c4b07" class="outline-3">
<h3 id="org22c4b07"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
<div id="outline-container-org761b288" class="outline-3">
<h3 id="org761b288"><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="orgb63ca55" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf711934" 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-orgbab5fbb" class="outline-2">
<h2 id="orgbab5fbb"><span class="section-number-2">4</span> Orbitals</h2>
<div id="outline-container-org49cdb83" class="outline-2">
<h2 id="org49cdb83"><span class="section-number-2">4</span> Orbitals</h2>
<div class="outline-text-2" id="text-4">
</div>
<div id="outline-container-org192cc6b" class="outline-3">
<h3 id="org192cc6b"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
<div id="outline-container-orge796f49" class="outline-3">
<h3 id="orge796f49"><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="org7053ccb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd71001a" 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-orgd7a38a5" class="outline-4">
<div id="outline-container-org257d059" 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="org33cb06a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org19fb4bd" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2097,7 +2097,7 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org9f64fa1" class="outline-4">
<div id="outline-container-org758e5b5" 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="orgc4ad110" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org1661a1c" 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-org157305a" class="outline-3">
<h3 id="org157305a"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div id="outline-container-orga2a9c35" class="outline-3">
<h3 id="orga2a9c35"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div class="outline-text-3" id="text-4-2">
<table id="org7c2dedf" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org4bd1de9" 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-org290677a" class="outline-4">
<h4 id="org290677a"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
<div id="outline-container-org02a784c" class="outline-4">
<h4 id="org02a784c"><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="org6e0e339" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org72bbbec" 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-orge26029c" class="outline-4">
<h4 id="orge26029c"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
<div id="outline-container-org5e866ba" class="outline-4">
<h4 id="org5e866ba"><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="org28046a0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2046201" 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-org868a479" class="outline-2">
<h2 id="org868a479"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div id="outline-container-orge99a418" class="outline-2">
<h2 id="orge99a418"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div class="outline-text-2" id="text-5">
</div>
<div id="outline-container-org2864ce0" class="outline-3">
<h3 id="org2864ce0"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
<div id="outline-container-orgd6c2373" class="outline-3">
<h3 id="orgd6c2373"><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="org274d61a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org7e28d19" 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-org84986f6" class="outline-3">
<h3 id="org84986f6"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
<div id="outline-container-org55c9b57" class="outline-3">
<h3 id="org55c9b57"><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="org895cdf5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc04d1d1" 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-org236c150" class="outline-3">
<h3 id="org236c150"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
<div id="outline-container-org7d6c586" class="outline-3">
<h3 id="org7d6c586"><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="orgdf72214" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org7be6391" 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-orgcf2e208" class="outline-3">
<h3 id="orgcf2e208"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
<div id="outline-container-orgbcb3817" class="outline-3">
<h3 id="orgbcb3817"><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="org2a193be" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org9da4ff6" 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-org7dc36b5" class="outline-2">
<h2 id="org7dc36b5"><span class="section-number-2">6</span> Correlation factors</h2>
<div id="outline-container-org22d7c18" class="outline-2">
<h2 id="org22d7c18"><span class="section-number-2">6</span> Correlation factors</h2>
<div class="outline-text-2" id="text-6">
</div>
<div id="outline-container-org4de43c8" class="outline-3">
<h3 id="org4de43c8"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
<div id="outline-container-org432fca4" class="outline-3">
<h3 id="org432fca4"><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-orgc9d1855" class="outline-4">
<h4 id="orgc9d1855"><span class="section-number-4">6.1.1</span> CHAMP</h4>
<div id="outline-container-org04b0804" class="outline-4">
<h4 id="org04b0804"><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-org163d71f" class="outline-4">
<h4 id="org163d71f"><span class="section-number-4">6.1.2</span> Mu</h4>
<div id="outline-container-org496e533" class="outline-4">
<h4 id="org496e533"><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="org8c75cc0"><span class="section-number-4">6.1.3</span> Table of values</h4>
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<h4 id="org1ca335f"><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="orgff41f26"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
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<h2 id="org66f0633"><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 19:59</p>
<p class="date">Created: 2024-08-17 Sat 20:27</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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