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README.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2024-10-17 Thu 17:27 -->
<!-- 2024-11-10 Sun 12:04 -->
<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: 2024-10-17 Thu 17:27</p>
<p class="date">Created: 2024-11-10 Sun 12:04</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>
<!-- 2024-10-17 Thu 17:27 -->
<!-- 2024-11-10 Sun 12:04 -->
<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="#orgd654dbe">1. Writing nuclear coordinates</a>
<li><a href="#orgf2dd36e">1. Writing nuclear coordinates</a>
<ul>
<li><a href="#orga7d7895">1.1. C</a></li>
<li><a href="#orgfe7eb4a">1.2. Python</a></li>
<li><a href="#org0463f5c">1.3. Fortran</a></li>
<li><a href="#org9f3540c">1.1. C</a></li>
<li><a href="#org2874c9f">1.2. Python</a></li>
<li><a href="#orga7805d4">1.3. Fortran</a></li>
</ul>
</li>
<li><a href="#orge3a2bc1">2. Accessing sparse quantities (integrals)</a>
<li><a href="#orgaf60a54">2. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#org75f0db0">2.1. Fortran</a>
<li><a href="#org97cb920">2.1. Fortran</a>
<ul>
<li><a href="#orgbf0742b">2.1.1. Declare Temporary variables</a></li>
<li><a href="#orgda8fbb6">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgc74a4bd">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org6ce7856">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org34fc4e8">2.1.5. Allocate memory</a></li>
<li><a href="#org3b8e00b">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org618da4e">2.1.7. Read two-electron quantities</a>
<li><a href="#org2cb0490">2.1.1. Declare Temporary variables</a></li>
<li><a href="#org6f29b41">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org5768f43">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org26967ee">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org740de11">2.1.5. Allocate memory</a></li>
<li><a href="#orgedd70c9">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org382a2c2">2.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#orgca48845">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org32e607f">2.1.7.2. Reduced density matrix</a></li>
<li><a href="#org9a34802">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org1bfab51">2.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#orgaf45320">2.1.8. Compute the energy</a></li>
<li><a href="#org4731a99">2.1.9. Terminate</a></li>
<li><a href="#org81852ba">2.1.8. Compute the energy</a></li>
<li><a href="#orged93321">2.1.9. Terminate</a></li>
</ul>
</li>
<li><a href="#orgd3b05cd">2.2. Python</a>
<li><a href="#org9ac57c1">2.2. Python</a>
<ul>
<li><a href="#orga83ff6b">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org59d098a">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#org93c61a1">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#orgda0362a">2.2.4. Read one-electron quantities</a></li>
<li><a href="#orgfddf953">2.2.5. Read two-electron quantities</a>
<li><a href="#org5272f95">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org381324f">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#org9af83ec">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#org9713c56">2.2.4. Read one-electron quantities</a></li>
<li><a href="#orge5f400c">2.2.5. Read two-electron quantities</a>
<ul>
<li><a href="#org3c973a9">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#org1949ad5">2.2.5.2. Reduced density matrix</a></li>
<li><a href="#orgc620a82">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#org9e1afc3">2.2.5.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org61c11b2">2.2.6. Compute the energy</a></li>
<li><a href="#org20ba188">2.2.6. Compute the energy</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#orgf27a8be">3. Reading determinants</a>
<li><a href="#org3442324">3. Reading determinants</a>
<ul>
<li><a href="#orgb223d21">3.1. Fortran</a></li>
<li><a href="#orga9cc058">3.1. Fortran</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-orgd654dbe" class="outline-2">
<h2 id="orgd654dbe"><span class="section-number-2">1</span> Writing nuclear coordinates</h2>
<div id="outline-container-orgf2dd36e" class="outline-2">
<h2 id="orgf2dd36e"><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-orga7d7895" class="outline-3">
<h3 id="orga7d7895"><span class="section-number-3">1.1</span> C</h3>
<div id="outline-container-org9f3540c" class="outline-3">
<h3 id="org9f3540c"><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-orgfe7eb4a" class="outline-3">
<h3 id="orgfe7eb4a"><span class="section-number-3">1.2</span> Python</h3>
<div id="outline-container-org2874c9f" class="outline-3">
<h3 id="org2874c9f"><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-org0463f5c" class="outline-3">
<h3 id="org0463f5c"><span class="section-number-3">1.3</span> Fortran</h3>
<div id="outline-container-orga7805d4" class="outline-3">
<h3 id="orga7805d4"><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-orge3a2bc1" class="outline-2">
<h2 id="orge3a2bc1"><span class="section-number-2">2</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-orgaf60a54" class="outline-2">
<h2 id="orgaf60a54"><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-org75f0db0" class="outline-3">
<h3 id="org75f0db0"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-org97cb920" class="outline-3">
<h3 id="org97cb920"><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-orgbf0742b" class="outline-4">
<h4 id="orgbf0742b"><span class="section-number-4">2.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-org2cb0490" class="outline-4">
<h4 id="org2cb0490"><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-orgda8fbb6" class="outline-4">
<h4 id="orgda8fbb6"><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-org6f29b41" class="outline-4">
<h4 id="org6f29b41"><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-orgc74a4bd" class="outline-4">
<h4 id="orgc74a4bd"><span class="section-number-4">2.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org5768f43" class="outline-4">
<h4 id="org5768f43"><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-org6ce7856" class="outline-4">
<h4 id="org6ce7856"><span class="section-number-4">2.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org26967ee" class="outline-4">
<h4 id="org26967ee"><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-org34fc4e8" class="outline-4">
<h4 id="org34fc4e8"><span class="section-number-4">2.1.5</span> Allocate memory</h4>
<div id="outline-container-org740de11" class="outline-4">
<h4 id="org740de11"><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-org3b8e00b" class="outline-4">
<h4 id="org3b8e00b"><span class="section-number-4">2.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-orgedd70c9" class="outline-4">
<h4 id="orgedd70c9"><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-org618da4e" class="outline-4">
<h4 id="org618da4e"><span class="section-number-4">2.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-org382a2c2" class="outline-4">
<h4 id="org382a2c2"><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-orgca48845" class="outline-5">
<h5 id="orgca48845"><span class="section-number-5">2.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org9a34802" class="outline-5">
<h5 id="org9a34802"><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-org32e607f" class="outline-5">
<h5 id="org32e607f"><span class="section-number-5">2.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org1bfab51" class="outline-5">
<h5 id="org1bfab51"><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-orgaf45320" class="outline-4">
<h4 id="orgaf45320"><span class="section-number-4">2.1.8</span> Compute the energy</h4>
<div id="outline-container-org81852ba" class="outline-4">
<h4 id="org81852ba"><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-org4731a99" class="outline-4">
<h4 id="org4731a99"><span class="section-number-4">2.1.9</span> Terminate</h4>
<div id="outline-container-orged93321" class="outline-4">
<h4 id="orged93321"><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-orgd3b05cd" class="outline-3">
<h3 id="orgd3b05cd"><span class="section-number-3">2.2</span> Python</h3>
<div id="outline-container-org9ac57c1" class="outline-3">
<h3 id="org9ac57c1"><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-orga83ff6b" class="outline-4">
<h4 id="orga83ff6b"><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-org5272f95" class="outline-4">
<h4 id="org5272f95"><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-org59d098a" class="outline-4">
<h4 id="org59d098a"><span class="section-number-4">2.2.2</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org381324f" class="outline-4">
<h4 id="org381324f"><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-org93c61a1" class="outline-4">
<h4 id="org93c61a1"><span class="section-number-4">2.2.3</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org9af83ec" class="outline-4">
<h4 id="org9af83ec"><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-orgda0362a" class="outline-4">
<h4 id="orgda0362a"><span class="section-number-4">2.2.4</span> Read one-electron quantities</h4>
<div id="outline-container-org9713c56" class="outline-4">
<h4 id="org9713c56"><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-orgfddf953" class="outline-4">
<h4 id="orgfddf953"><span class="section-number-4">2.2.5</span> Read two-electron quantities</h4>
<div id="outline-container-orge5f400c" class="outline-4">
<h4 id="orge5f400c"><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-org3c973a9" class="outline-5">
<h5 id="org3c973a9"><span class="section-number-5">2.2.5.1</span> Electron repulsion integrals</h5>
<div id="outline-container-orgc620a82" class="outline-5">
<h5 id="orgc620a82"><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-org1949ad5" class="outline-5">
<h5 id="org1949ad5"><span class="section-number-5">2.2.5.2</span> Reduced density matrix</h5>
<div id="outline-container-org9e1afc3" class="outline-5">
<h5 id="org9e1afc3"><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-org61c11b2" class="outline-4">
<h4 id="org61c11b2"><span class="section-number-4">2.2.6</span> Compute the energy</h4>
<div id="outline-container-org20ba188" class="outline-4">
<h4 id="org20ba188"><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-orgf27a8be" class="outline-2">
<h2 id="orgf27a8be"><span class="section-number-2">3</span> Reading determinants</h2>
<div id="outline-container-org3442324" class="outline-2">
<h2 id="org3442324"><span class="section-number-2">3</span> Reading determinants</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-orgb223d21" class="outline-3">
<h3 id="orgb223d21"><span class="section-number-3">3.1</span> Fortran</h3>
<div id="outline-container-orga9cc058" class="outline-3">
<h3 id="orga9cc058"><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: 2024-10-17 Thu 17:27</p>
<p class="date">Created: 2024-11-10 Sun 12:04</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>
<!-- 2024-10-17 Thu 17:27 -->
<!-- 2024-11-10 Sun 12:04 -->
<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: 2024-10-17 Thu 17:27</p>
<p class="date">Created: 2024-11-10 Sun 12:04</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>
<!-- 2024-10-17 Thu 17:27 -->
<!-- 2024-11-10 Sun 12:04 -->
<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: 2024-10-17 Thu 17:27</p>
<p class="date">Created: 2024-11-10 Sun 12:04</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

58
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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2024-10-17 Thu 17:27 -->
<!-- 2024-11-10 Sun 12:04 -->
<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="#orgc4e45a1">1. Format specification</a>
<li><a href="#org33d2744">1. Format specification</a>
<ul>
<li><a href="#org8c33c4d">1.1. Organization of the data</a></li>
<li><a href="#org9b57f35">1.2. Data types</a></li>
<li><a href="#org8b849c1">1.1. Organization of the data</a></li>
<li><a href="#org091cc14">1.2. Data types</a></li>
</ul>
</li>
<li><a href="#org757c768">2. The TREXIO library</a>
<li><a href="#org7bbccf5">2. The TREXIO library</a>
<ul>
<li><a href="#orgfce671a">2.1. The front-end</a></li>
<li><a href="#org5a60e88">2.2. The back-end</a></li>
<li><a href="#org0328c24">2.3. Supported languages</a></li>
<li><a href="#org92a552a">2.4. Source code generation and documentation</a></li>
<li><a href="#orgbd65044">2.5. Availability</a></li>
<li><a href="#org49a4c99">2.1. The front-end</a></li>
<li><a href="#orga064d91">2.2. The back-end</a></li>
<li><a href="#orgfa5df69">2.3. Supported languages</a></li>
<li><a href="#org38f6afb">2.4. Source code generation and documentation</a></li>
<li><a href="#org8d92bf1">2.5. Availability</a></li>
</ul>
</li>
</ul>
@ -366,8 +366,8 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-orgc4e45a1" class="outline-2">
<h2 id="orgc4e45a1"><span class="section-number-2">1</span> Format specification</h2>
<div id="outline-container-org33d2744" class="outline-2">
<h2 id="org33d2744"><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-org8c33c4d" class="outline-3">
<h3 id="org8c33c4d"><span class="section-number-3">1.1</span> Organization of the data</h3>
<div id="outline-container-org8b849c1" class="outline-3">
<h3 id="org8b849c1"><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-org9b57f35" class="outline-3">
<h3 id="org9b57f35"><span class="section-number-3">1.2</span> Data types</h3>
<div id="outline-container-org091cc14" class="outline-3">
<h3 id="org091cc14"><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-org757c768" class="outline-2">
<h2 id="org757c768"><span class="section-number-2">2</span> The TREXIO library</h2>
<div id="outline-container-org7bbccf5" class="outline-2">
<h2 id="org7bbccf5"><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-orgfce671a" class="outline-3">
<h3 id="orgfce671a"><span class="section-number-3">2.1</span> The front-end</h3>
<div id="outline-container-org49a4c99" class="outline-3">
<h3 id="org49a4c99"><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-org5a60e88" class="outline-3">
<h3 id="org5a60e88"><span class="section-number-3">2.2</span> The back-end</h3>
<div id="outline-container-orga064d91" class="outline-3">
<h3 id="orga064d91"><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-org0328c24" class="outline-3">
<h3 id="org0328c24"><span class="section-number-3">2.3</span> Supported languages</h3>
<div id="outline-container-orgfa5df69" class="outline-3">
<h3 id="orgfa5df69"><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-org92a552a" class="outline-3">
<h3 id="org92a552a"><span class="section-number-3">2.4</span> Source code generation and documentation</h3>
<div id="outline-container-org38f6afb" class="outline-3">
<h3 id="org38f6afb"><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-orgbd65044" class="outline-3">
<h3 id="orgbd65044"><span class="section-number-3">2.5</span> Availability</h3>
<div id="outline-container-org8d92bf1" class="outline-3">
<h3 id="org8d92bf1"><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: 2024-10-17 Thu 17:27</p>
<p class="date">Created: 2024-11-10 Sun 12:04</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>
<!-- 2024-10-17 Thu 17:27 -->
<!-- 2024-11-10 Sun 12:04 -->
<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="#org0edc2d5">1. Template for HDF5 definitions</a></li>
<li><a href="#org0ab0033">2. Template for HDF5 structures</a></li>
<li><a href="#org804a868">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org900f971">4. Template for HDF5 has a group</a></li>
<li><a href="#org57a0835">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org582f9a2">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#orgdbacd08">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#orgfe95cc8">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#orge0a28f4">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org3fd3b62">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org9d1778f">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org0c6d038">12. Source code for the determinant part</a></li>
<li><a href="#org1388929">13. Helper functions</a></li>
<li><a href="#org4125529">1. Template for HDF5 definitions</a></li>
<li><a href="#orge53dadb">2. Template for HDF5 structures</a></li>
<li><a href="#org2977245">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org973a8fd">4. Template for HDF5 has a group</a></li>
<li><a href="#orgd355559">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orge3e27e9">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org2cfef52">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org4997150">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#orge3ea724">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org74657a9">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#orge880ab1">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org720abcf">12. Source code for the determinant part</a></li>
<li><a href="#org7833849">13. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-org0edc2d5" class="outline-2">
<h2 id="org0edc2d5"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-org4125529" class="outline-2">
<h2 id="org4125529"><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-org0ab0033" class="outline-2">
<h2 id="org0ab0033"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-orge53dadb" class="outline-2">
<h2 id="orge53dadb"><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-org804a868" class="outline-2">
<h2 id="org804a868"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-org2977245" class="outline-2">
<h2 id="org2977245"><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-org900f971" class="outline-2">
<h2 id="org900f971"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-org973a8fd" class="outline-2">
<h2 id="org973a8fd"><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-org57a0835" class="outline-2">
<h2 id="org57a0835"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-orgd355559" class="outline-2">
<h2 id="orgd355559"><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-org582f9a2" class="outline-2">
<h2 id="org582f9a2"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-orge3e27e9" class="outline-2">
<h2 id="orge3e27e9"><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-orgdbacd08" class="outline-2">
<h2 id="orgdbacd08"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-org2cfef52" class="outline-2">
<h2 id="org2cfef52"><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-orgfe95cc8" class="outline-2">
<h2 id="orgfe95cc8"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div id="outline-container-org4997150" class="outline-2">
<h2 id="org4997150"><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-orge0a28f4" class="outline-2">
<h2 id="orge0a28f4"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-orge3ea724" class="outline-2">
<h2 id="orge3ea724"><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-org3fd3b62" class="outline-2">
<h2 id="org3fd3b62"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-org74657a9" class="outline-2">
<h2 id="org74657a9"><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-org9d1778f" class="outline-2">
<h2 id="org9d1778f"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-orge880ab1" class="outline-2">
<h2 id="orge880ab1"><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-org0c6d038" class="outline-2">
<h2 id="org0c6d038"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div id="outline-container-org720abcf" class="outline-2">
<h2 id="org720abcf"><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-org1388929" class="outline-2">
<h2 id="org1388929"><span class="section-number-2">13</span> Helper functions</h2>
<div id="outline-container-org7833849" class="outline-2">
<h2 id="org7833849"><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: 2024-10-17 Thu 17:27</p>
<p class="date">Created: 2024-11-10 Sun 12:04</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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<title>TEXT back end</title>
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<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#org7752b66">1. Template for group-related structures in text back end</a></li>
<li><a href="#org3f5b689">2. Template for general structure in text back end</a></li>
<li><a href="#org5966b9b">3. Initialize function (constant part)</a></li>
<li><a href="#orgca96540">4. Deinitialize function (templated part)</a></li>
<li><a href="#org52e5c5b">5. Flush function (templated part)</a></li>
<li><a href="#org8374413">6. Template for text read a group</a></li>
<li><a href="#org9e600e9">7. Template for text has a group</a></li>
<li><a href="#org7838127">8. Template for text flush a group</a></li>
<li><a href="#org1e0c989">9. Template for text free memory</a></li>
<li><a href="#org3b71508">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orgf9aa76e">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org9fcae23">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#orgd9f855c">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org4031bc9">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org4313710">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#orgf89314f">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org6a0e512">17. Source code for the determinant part</a></li>
<li><a href="#org368939d">1. Template for group-related structures in text back end</a></li>
<li><a href="#org827421f">2. Template for general structure in text back end</a></li>
<li><a href="#orgb0327dc">3. Initialize function (constant part)</a></li>
<li><a href="#org54d9e31">4. Deinitialize function (templated part)</a></li>
<li><a href="#org3959b7d">5. Flush function (templated part)</a></li>
<li><a href="#org58ad3da">6. Template for text read a group</a></li>
<li><a href="#org0e9a7d3">7. Template for text has a group</a></li>
<li><a href="#org5b22272">8. Template for text flush a group</a></li>
<li><a href="#orgce75245">9. Template for text free memory</a></li>
<li><a href="#orgb052c42">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org5dd3267">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orgb7759ae">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org1967414">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org1edba36">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org5e8fdb5">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#orgf1f1ead">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org9ae9c2a">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-org7752b66" class="outline-2">
<h2 id="org7752b66"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-org368939d" class="outline-2">
<h2 id="org368939d"><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-org3f5b689" class="outline-2">
<h2 id="org3f5b689"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-org827421f" class="outline-2">
<h2 id="org827421f"><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-org5966b9b" class="outline-2">
<h2 id="org5966b9b"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-orgb0327dc" class="outline-2">
<h2 id="orgb0327dc"><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-orgca96540" class="outline-2">
<h2 id="orgca96540"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-org54d9e31" class="outline-2">
<h2 id="org54d9e31"><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-org52e5c5b" class="outline-2">
<h2 id="org52e5c5b"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div id="outline-container-org3959b7d" class="outline-2">
<h2 id="org3959b7d"><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-org8374413" class="outline-2">
<h2 id="org8374413"><span class="section-number-2">6</span> Template for text read a group</h2>
<div id="outline-container-org58ad3da" class="outline-2">
<h2 id="org58ad3da"><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-org9e600e9" class="outline-2">
<h2 id="org9e600e9"><span class="section-number-2">7</span> Template for text has a group</h2>
<div id="outline-container-org0e9a7d3" class="outline-2">
<h2 id="org0e9a7d3"><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-org7838127" class="outline-2">
<h2 id="org7838127"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div id="outline-container-org5b22272" class="outline-2">
<h2 id="org5b22272"><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-org1e0c989" class="outline-2">
<h2 id="org1e0c989"><span class="section-number-2">9</span> Template for text free memory</h2>
<div id="outline-container-orgce75245" class="outline-2">
<h2 id="orgce75245"><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-org3b71508" class="outline-2">
<h2 id="org3b71508"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-orgb052c42" class="outline-2">
<h2 id="orgb052c42"><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-orgf9aa76e" class="outline-2">
<h2 id="orgf9aa76e"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-org5dd3267" class="outline-2">
<h2 id="org5dd3267"><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-org9fcae23" class="outline-2">
<h2 id="org9fcae23"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-orgb7759ae" class="outline-2">
<h2 id="orgb7759ae"><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-orgd9f855c" class="outline-2">
<h2 id="orgd9f855c"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-org1967414" class="outline-2">
<h2 id="org1967414"><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-org4031bc9" class="outline-2">
<h2 id="org4031bc9"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-org1edba36" class="outline-2">
<h2 id="org1edba36"><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-org4313710" class="outline-2">
<h2 id="org4313710"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div id="outline-container-org5e8fdb5" class="outline-2">
<h2 id="org5e8fdb5"><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-orgf89314f" class="outline-2">
<h2 id="orgf89314f"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-orgf1f1ead" class="outline-2">
<h2 id="orgf1f1ead"><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-org6a0e512" class="outline-2">
<h2 id="org6a0e512"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div id="outline-container-org9ae9c2a" class="outline-2">
<h2 id="org9ae9c2a"><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: 2024-10-17 Thu 17:27</p>
<p class="date">Created: 2024-11-10 Sun 12:04</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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<head>
<!-- 2024-10-17 Thu 17:27 -->
<!-- 2024-11-10 Sun 12:04 -->
<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="#org73b4ea6">1. Metadata (metadata group)</a></li>
<li><a href="#org87ab976">2. System</a>
<li><a href="#orge0c91eb">1. Metadata (metadata group)</a></li>
<li><a href="#orgb1b7cae">2. System</a>
<ul>
<li><a href="#org3171190">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org219dd9d">2.2. Cell (cell group)</a></li>
<li><a href="#org6ff9bd3">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#orgb8abd4a">2.4. Electron (electron group)</a></li>
<li><a href="#org935331a">2.5. Ground or excited states (state group)</a></li>
<li><a href="#org7701ff8">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#orga054d11">2.2. Cell (cell group)</a></li>
<li><a href="#org4626f53">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org24c09f0">2.4. Electron (electron group)</a></li>
<li><a href="#orgf38e06c">2.5. Ground or excited states (state group)</a></li>
</ul>
</li>
<li><a href="#org7984b2a">3. Basis functions</a>
<li><a href="#orgb0ea228">3. Basis functions</a>
<ul>
<li><a href="#org626d57d">3.1. Basis set (basis group)</a>
<li><a href="#org7387e20">3.1. Basis set (basis group)</a>
<ul>
<li><a href="#org10a7da7">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#org78f82e1">3.1.2. Numerical orbitals</a></li>
<li><a href="#org3f8c5c6">3.1.3. Plane waves</a></li>
<li><a href="#org4ec1368">3.1.4. Oscillating orbitals</a></li>
<li><a href="#orgbe9691e">3.1.5. Data definitions</a></li>
<li><a href="#orgde706a6">3.1.6. Example</a></li>
<li><a href="#org9e5aaf1">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#org893af82">3.1.2. Numerical orbitals</a></li>
<li><a href="#orge7516dd">3.1.3. Plane waves</a></li>
<li><a href="#orgb89f369">3.1.4. Oscillating orbitals</a></li>
<li><a href="#orgcb0aff6">3.1.5. Data definitions</a></li>
<li><a href="#org01f247b">3.1.6. Example</a></li>
</ul>
</li>
<li><a href="#orgc4d7902">3.2. Effective core potentials (ecp group)</a>
<li><a href="#org1413ea5">3.2. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#orgaac916a">3.2.1. Example</a></li>
<li><a href="#orge1b0563">3.2.1. Example</a></li>
</ul>
</li>
<li><a href="#orgde266ab">3.3. Numerical integration grid (grid group)</a></li>
<li><a href="#org3530dd0">3.3. Numerical integration grid (grid group)</a></li>
</ul>
</li>
<li><a href="#org966b3ca">4. Orbitals</a>
<li><a href="#org3e3cc27">4. Orbitals</a>
<ul>
<li><a href="#orgc4ebd24">4.1. Atomic orbitals (ao group)</a>
<li><a href="#org848e699">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="#orgf8df7bf">4.2. Molecular orbitals (mo group)</a>
<li><a href="#orgeef6e28">4.2. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#orgb842f6a">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orga252e7e">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org8da381b">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org49ac495">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org3c10eb2">5. Multi-determinant information</a>
<li><a href="#org441f795">5. Multi-determinant information</a>
<ul>
<li><a href="#org7bb7a91">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org1a192d3">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#orgd943d13">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org195d1a9">5.4. Reduced density matrices (rdm group)</a></li>
<li><a href="#org65ed167">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#orge22e2ac">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#orgaf8bc0d">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org3dcdeb7">5.4. Reduced density matrices (rdm group)</a></li>
</ul>
</li>
<li><a href="#orga674974">6. Correlation factors</a>
<li><a href="#org337872b">6. Correlation factors</a>
<ul>
<li><a href="#orgf9adf09">6.1. Jastrow factor (jastrow group)</a>
<li><a href="#org538fa8d">6.1. Jastrow factor (jastrow group)</a>
<ul>
<li><a href="#org27e88c4">6.1.1. CHAMP</a></li>
<li><a href="#org8e564ce">6.1.2. Mu</a></li>
<li><a href="#orgd449d36">6.1.3. Table of values</a></li>
<li><a href="#orge74811a">6.1.1. CHAMP</a></li>
<li><a href="#org16c6488">6.1.2. Mu</a></li>
<li><a href="#org7fd5d8f">6.1.3. Table of values</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org0144004">7. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#org58453ba">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-org73b4ea6" class="outline-2">
<h2 id="org73b4ea6"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-orge0c91eb" class="outline-2">
<h2 id="orge0c91eb"><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="orgb85bd43" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org675a902" 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-org87ab976" class="outline-2">
<h2 id="org87ab976"><span class="section-number-2">2</span> System</h2>
<div id="outline-container-orgb1b7cae" class="outline-2">
<h2 id="orgb1b7cae"><span class="section-number-2">2</span> System</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-org3171190" class="outline-3">
<h3 id="org3171190"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
<div id="outline-container-org7701ff8" class="outline-3">
<h3 id="org7701ff8"><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="org70fd1a6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org7618a71" 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-org219dd9d" class="outline-3">
<h3 id="org219dd9d"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
<div id="outline-container-orga054d11" class="outline-3">
<h3 id="orga054d11"><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="org788458f" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org8efdbfd" 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-org6ff9bd3" class="outline-3">
<h3 id="org6ff9bd3"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div id="outline-container-org4626f53" class="outline-3">
<h3 id="org4626f53"><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="org3cb9f6b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2c7405b" 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-orgb8abd4a" class="outline-3">
<h3 id="orgb8abd4a"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
<div id="outline-container-org24c09f0" class="outline-3">
<h3 id="org24c09f0"><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="org4805ee4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2076992" 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-org935331a" class="outline-3">
<h3 id="org935331a"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
<div id="outline-container-orgf38e06c" class="outline-3">
<h3 id="orgf38e06c"><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="org50223f3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgdcc77b2" 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-org7984b2a" class="outline-2">
<h2 id="org7984b2a"><span class="section-number-2">3</span> Basis functions</h2>
<div id="outline-container-orgb0ea228" class="outline-2">
<h2 id="orgb0ea228"><span class="section-number-2">3</span> Basis functions</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org626d57d" class="outline-3">
<h3 id="org626d57d"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
<div id="outline-container-org7387e20" class="outline-3">
<h3 id="org7387e20"><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-org10a7da7" class="outline-4">
<h4 id="org10a7da7"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
<div id="outline-container-org9e5aaf1" class="outline-4">
<h4 id="org9e5aaf1"><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-org78f82e1" class="outline-4">
<h4 id="org78f82e1"><span class="section-number-4">3.1.2</span> Numerical orbitals</h4>
<div id="outline-container-org893af82" class="outline-4">
<h4 id="org893af82"><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-org3f8c5c6" class="outline-4">
<h4 id="org3f8c5c6"><span class="section-number-4">3.1.3</span> Plane waves</h4>
<div id="outline-container-orge7516dd" class="outline-4">
<h4 id="orge7516dd"><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-org4ec1368" class="outline-4">
<h4 id="org4ec1368"><span class="section-number-4">3.1.4</span> Oscillating orbitals</h4>
<div id="outline-container-orgb89f369" class="outline-4">
<h4 id="orgb89f369"><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-orgbe9691e" class="outline-4">
<h4 id="orgbe9691e"><span class="section-number-4">3.1.5</span> Data definitions</h4>
<div id="outline-container-orgcb0aff6" class="outline-4">
<h4 id="orgcb0aff6"><span class="section-number-4">3.1.5</span> Data definitions</h4>
<div class="outline-text-4" id="text-3-1-5">
<table id="orgf13fa1d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org6420308" 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-orgde706a6" class="outline-4">
<h4 id="orgde706a6"><span class="section-number-4">3.1.6</span> Example</h4>
<div id="outline-container-org01f247b" class="outline-4">
<h4 id="org01f247b"><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-orgc4d7902" class="outline-3">
<h3 id="orgc4d7902"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
<div id="outline-container-org1413ea5" class="outline-3">
<h3 id="org1413ea5"><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="org82a2186" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org0ce9df2" 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-orgaac916a" class="outline-4">
<h4 id="orgaac916a"><span class="section-number-4">3.2.1</span> Example</h4>
<div id="outline-container-orge1b0563" class="outline-4">
<h4 id="orge1b0563"><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-orgde266ab" class="outline-3">
<h3 id="orgde266ab"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
<div id="outline-container-org3530dd0" class="outline-3">
<h3 id="org3530dd0"><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="orge9fde05" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5bf93c4" 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-org966b3ca" class="outline-2">
<h2 id="org966b3ca"><span class="section-number-2">4</span> Orbitals</h2>
<div id="outline-container-org3e3cc27" class="outline-2">
<h2 id="org3e3cc27"><span class="section-number-2">4</span> Orbitals</h2>
<div class="outline-text-2" id="text-4">
</div>
<div id="outline-container-orgc4ebd24" class="outline-3">
<h3 id="orgc4ebd24"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
<div id="outline-container-org848e699" class="outline-3">
<h3 id="org848e699"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
<div class="outline-text-3" id="text-4-1">
<p>
AOs are defined as
@ -1918,7 +1918,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</p>
<table id="org50aaf7c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgcc3a92b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1977,7 +1977,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</table>
</div>
<div id="outline-container-org23844c5" class="outline-4">
<div id="outline-container-org93319a7" class="outline-4">
<h4 id="ao_one_e"><span class="section-number-4">4.1.1</span> One-electron integrals (<code>ao_1e_int</code> group)</h4>
<div class="outline-text-4" id="text-ao_one_e">
<ul class="org-ul">
@ -1995,7 +1995,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="org465425b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb180a50" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2103,7 +2103,7 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org4dcd6db" class="outline-4">
<div id="outline-container-org3d4fc30" class="outline-4">
<h4 id="ao_two_e"><span class="section-number-4">4.1.2</span> Two-electron integrals (<code>ao_2e_int</code> group)</h4>
<div class="outline-text-4" id="text-ao_two_e">
<p>
@ -2129,7 +2129,7 @@ The Cholesky decomposition of the integrals can also be stored:
\]
</p>
<table id="org7417e8c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org09a53be" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2206,10 +2206,10 @@ The Cholesky decomposition of the integrals can also be stored:
</div>
</div>
<div id="outline-container-orgf8df7bf" class="outline-3">
<h3 id="orgf8df7bf"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div id="outline-container-orgeef6e28" class="outline-3">
<h3 id="orgeef6e28"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div class="outline-text-3" id="text-4-2">
<table id="org6bb79ee" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org1589f1c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2325,8 +2325,8 @@ is the number of spin-orbitals, twice the number of spatial orbitals.
</div>
<div id="outline-container-orgb842f6a" class="outline-4">
<h4 id="orgb842f6a"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
<div id="outline-container-org8da381b" class="outline-4">
<h4 id="org8da381b"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
<div class="outline-text-4" id="text-4-2-1">
<p>
The operators as the same as those defined in the
@ -2334,7 +2334,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org0601716" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org4397338" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2442,8 +2442,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-orga252e7e" class="outline-4">
<h4 id="orga252e7e"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
<div id="outline-container-org49ac495" class="outline-4">
<h4 id="org49ac495"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
<div class="outline-text-4" id="text-4-2-2">
<p>
The operators are the same as those defined in the
@ -2451,7 +2451,7 @@ The operators are the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org9c9099a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf5306f2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2529,12 +2529,12 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org3c10eb2" class="outline-2">
<h2 id="org3c10eb2"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div id="outline-container-org441f795" class="outline-2">
<h2 id="org441f795"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div class="outline-text-2" id="text-5">
</div>
<div id="outline-container-org7bb7a91" class="outline-3">
<h3 id="org7bb7a91"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
<div id="outline-container-org65ed167" class="outline-3">
<h3 id="org65ed167"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
<div class="outline-text-3" id="text-5-1">
<p>
The configuration interaction (CI) wave function \(\Psi\)
@ -2576,7 +2576,7 @@ produced by the code generator.
An illustration on how to read determinants is presented in the <a href="./examples.html">examples</a>.
</p>
<table id="orgaca8f07" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org35c0305" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2628,8 +2628,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
</div>
</div>
<div id="outline-container-org1a192d3" class="outline-3">
<h3 id="org1a192d3"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
<div id="outline-container-orge22e2ac" class="outline-3">
<h3 id="orge22e2ac"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
<div class="outline-text-3" id="text-5-2">
<p>
The configuration interaction (CI) wave function \(\Psi\) can be
@ -2651,7 +2651,7 @@ matrix \(\langle D_I | \psi_J \rangle\) needed to project the CSFs in
the basis of Slater determinants.
</p>
<table id="org8731827" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org9e854ed" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2703,8 +2703,8 @@ the basis of Slater determinants.
</div>
</div>
<div id="outline-container-orgd943d13" class="outline-3">
<h3 id="orgd943d13"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
<div id="outline-container-orgaf8bc0d" class="outline-3">
<h3 id="orgaf8bc0d"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
<div class="outline-text-3" id="text-5-3">
<p>
The wave function may be expressed in terms of action of the cluster
@ -2775,7 +2775,7 @@ The order of the indices is chosen such that
<li>\(\dots\)</li>
</ul>
<table id="orge701b19" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgde12823" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2867,8 +2867,8 @@ The order of the indices is chosen such that
</div>
</div>
<div id="outline-container-org195d1a9" class="outline-3">
<h3 id="org195d1a9"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
<div id="outline-container-org3dcdeb7" class="outline-3">
<h3 id="org3dcdeb7"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
<div class="outline-text-3" id="text-5-4">
<p>
The reduced density matrices are defined in the basis of molecular
@ -2940,7 +2940,7 @@ expressed in a basis of a one-electron function
\(g_{ik}(\mathbf{r}_1) = \phi_i(\mathbf{r}_1) \phi_k(\mathbf{r}_1)\).
</p>
<table id="org7085d39" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgeb33edd" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -3105,12 +3105,12 @@ expressed in a basis of a one-electron function
</div>
</div>
<div id="outline-container-orga674974" class="outline-2">
<h2 id="orga674974"><span class="section-number-2">6</span> Correlation factors</h2>
<div id="outline-container-org337872b" class="outline-2">
<h2 id="org337872b"><span class="section-number-2">6</span> Correlation factors</h2>
<div class="outline-text-2" id="text-6">
</div>
<div id="outline-container-orgf9adf09" class="outline-3">
<h3 id="orgf9adf09"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
<div id="outline-container-org538fa8d" class="outline-3">
<h3 id="org538fa8d"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
<div class="outline-text-3" id="text-6-1">
<p>
The Jastrow factor is an $N$-electron function which multiplies the CI
@ -3135,8 +3135,8 @@ following:
</ul>
</div>
<div id="outline-container-org27e88c4" class="outline-4">
<h4 id="org27e88c4"><span class="section-number-4">6.1.1</span> CHAMP</h4>
<div id="outline-container-orge74811a" class="outline-4">
<h4 id="orge74811a"><span class="section-number-4">6.1.1</span> CHAMP</h4>
<div class="outline-text-4" id="text-6-1-1">
<p>
The first form of Jastrow factor is the one used in
@ -3237,8 +3237,8 @@ The terms \(J_{\text{ee},ij}^\infty\) and \(J_{\text{eN}}^\infty\) are shifts to
</div>
<div id="outline-container-org8e564ce" class="outline-4">
<h4 id="org8e564ce"><span class="section-number-4">6.1.2</span> Mu</h4>
<div id="outline-container-org16c6488" class="outline-4">
<h4 id="org16c6488"><span class="section-number-4">6.1.2</span> Mu</h4>
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<p>
<a href="https://aip.scitation.org/doi/10.1063/5.0044683">Mu-Jastrow</a> is based on a one-parameter correlation factor that has
@ -3335,10 +3335,10 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
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<h4 id="orgd449d36"><span class="section-number-4">6.1.3</span> Table of values</h4>
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<h4 id="org7fd5d8f"><span class="section-number-4">6.1.3</span> Table of values</h4>
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@ -3456,8 +3456,8 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
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<h2 id="org0144004"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
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<h2 id="org58453ba"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
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<p>
In quantum Monte Carlo calculations, the wave function is evaluated
@ -3471,7 +3471,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
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@ -3533,7 +3533,7 @@ of $&uarr;$-spin and then all the $&darr;$-spin.
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<div id="postamble" class="status">
<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2024-10-17 Thu 17:27</p>
<p class="date">Created: 2024-11-10 Sun 12:04</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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