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README.html
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<head>
<!-- 2023-05-22 Mon 10:11 -->
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<meta http-equiv="Content-Type" content="text/html;charset=utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<title>TREXIO source code documentation</title>
@ -383,7 +383,7 @@ 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: 2023-05-22 Mon 10:11</p>
<p class="date">Created: 2023-06-02 Fri 12:01</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>
<!-- 2023-05-22 Mon 10:11 -->
<!-- 2023-06-02 Fri 12:01 -->
<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="#org3586347">1. Writing nuclear coordinates</a>
<li><a href="#org7c03505">1. Writing nuclear coordinates</a>
<ul>
<li><a href="#orgc8b3cff">1.1. C</a></li>
<li><a href="#org7446658">1.2. Python</a></li>
<li><a href="#org9eb62f4">1.3. Fortran</a></li>
<li><a href="#org307c5bd">1.1. C</a></li>
<li><a href="#org8d00104">1.2. Python</a></li>
<li><a href="#org3830732">1.3. Fortran</a></li>
</ul>
</li>
<li><a href="#org39a9d66">2. Accessing sparse quantities (integrals)</a>
<li><a href="#orgffa8771">2. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#org463265d">2.1. Fortran</a>
<li><a href="#orgf80eefd">2.1. Fortran</a>
<ul>
<li><a href="#orge79eea4">2.1.1. Declare Temporary variables</a></li>
<li><a href="#org37ad15c">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org0b71c90">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orgc71c328">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org1bd58ba">2.1.5. Allocate memory</a></li>
<li><a href="#org9afacf8">2.1.6. Read one-electron quantities</a></li>
<li><a href="#orgdd82a02">2.1.7. Read two-electron quantities</a>
<li><a href="#orgc2f2fb6">2.1.1. Declare Temporary variables</a></li>
<li><a href="#org3f71f75">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org3833a87">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#orgc611005">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org5469e6f">2.1.5. Allocate memory</a></li>
<li><a href="#org8916ffd">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org53d79e4">2.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#orga3e43ab">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org910acca">2.1.7.2. Reduced density matrix</a></li>
<li><a href="#org55a613b">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org1ac8665">2.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#orgc50702a">2.1.8. Compute the energy</a></li>
<li><a href="#org8a2c477">2.1.9. Terminate</a></li>
<li><a href="#orgf460f20">2.1.8. Compute the energy</a></li>
<li><a href="#orgc0803d9">2.1.9. Terminate</a></li>
</ul>
</li>
<li><a href="#orge79e488">2.2. Python</a>
<li><a href="#org5f26da5">2.2. Python</a>
<ul>
<li><a href="#orgd2ed92b">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org221a287">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#org296c21c">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#orgce97720">2.2.4. Read one-electron quantities</a></li>
<li><a href="#org13b8ae6">2.2.5. Read two-electron quantities</a>
<li><a href="#org25629b4">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orga0220c6">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#org4d823b6">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#org6d75653">2.2.4. Read one-electron quantities</a></li>
<li><a href="#org79f50e2">2.2.5. Read two-electron quantities</a>
<ul>
<li><a href="#org05aa76b">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#org7443645">2.2.5.2. Reduced density matrix</a></li>
<li><a href="#orgabfc1a5">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#orgb218809">2.2.5.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#orgdb01e8f">2.2.6. Compute the energy</a></li>
<li><a href="#org4317d8b">2.2.6. Compute the energy</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org452836b">3. Reading determinants</a>
<li><a href="#org21b1c8e">3. Reading determinants</a>
<ul>
<li><a href="#orgb4e548b">3.1. Fortran</a></li>
<li><a href="#orgc8b0db1">3.1. Fortran</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-org3586347" class="outline-2">
<h2 id="org3586347"><span class="section-number-2">1</span> Writing nuclear coordinates</h2>
<div id="outline-container-org7c03505" class="outline-2">
<h2 id="org7c03505"><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-orgc8b3cff" class="outline-3">
<h3 id="orgc8b3cff"><span class="section-number-3">1.1</span> C</h3>
<div id="outline-container-org307c5bd" class="outline-3">
<h3 id="org307c5bd"><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-org7446658" class="outline-3">
<h3 id="org7446658"><span class="section-number-3">1.2</span> Python</h3>
<div id="outline-container-org8d00104" class="outline-3">
<h3 id="org8d00104"><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-org9eb62f4" class="outline-3">
<h3 id="org9eb62f4"><span class="section-number-3">1.3</span> Fortran</h3>
<div id="outline-container-org3830732" class="outline-3">
<h3 id="org3830732"><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-org39a9d66" class="outline-2">
<h2 id="org39a9d66"><span class="section-number-2">2</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-orgffa8771" class="outline-2">
<h2 id="orgffa8771"><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-org463265d" class="outline-3">
<h3 id="org463265d"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-orgf80eefd" class="outline-3">
<h3 id="orgf80eefd"><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-orge79eea4" class="outline-4">
<h4 id="orge79eea4"><span class="section-number-4">2.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-orgc2f2fb6" class="outline-4">
<h4 id="orgc2f2fb6"><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-org37ad15c" class="outline-4">
<h4 id="org37ad15c"><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-org3f71f75" class="outline-4">
<h4 id="org3f71f75"><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-org0b71c90" class="outline-4">
<h4 id="org0b71c90"><span class="section-number-4">2.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org3833a87" class="outline-4">
<h4 id="org3833a87"><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-orgc71c328" class="outline-4">
<h4 id="orgc71c328"><span class="section-number-4">2.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-orgc611005" class="outline-4">
<h4 id="orgc611005"><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-org1bd58ba" class="outline-4">
<h4 id="org1bd58ba"><span class="section-number-4">2.1.5</span> Allocate memory</h4>
<div id="outline-container-org5469e6f" class="outline-4">
<h4 id="org5469e6f"><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-org9afacf8" class="outline-4">
<h4 id="org9afacf8"><span class="section-number-4">2.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org8916ffd" class="outline-4">
<h4 id="org8916ffd"><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-orgdd82a02" class="outline-4">
<h4 id="orgdd82a02"><span class="section-number-4">2.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-org53d79e4" class="outline-4">
<h4 id="org53d79e4"><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-orga3e43ab" class="outline-5">
<h5 id="orga3e43ab"><span class="section-number-5">2.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org55a613b" class="outline-5">
<h5 id="org55a613b"><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-org910acca" class="outline-5">
<h5 id="org910acca"><span class="section-number-5">2.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org1ac8665" class="outline-5">
<h5 id="org1ac8665"><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-orgc50702a" class="outline-4">
<h4 id="orgc50702a"><span class="section-number-4">2.1.8</span> Compute the energy</h4>
<div id="outline-container-orgf460f20" class="outline-4">
<h4 id="orgf460f20"><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-org8a2c477" class="outline-4">
<h4 id="org8a2c477"><span class="section-number-4">2.1.9</span> Terminate</h4>
<div id="outline-container-orgc0803d9" class="outline-4">
<h4 id="orgc0803d9"><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-orge79e488" class="outline-3">
<h3 id="orge79e488"><span class="section-number-3">2.2</span> Python</h3>
<div id="outline-container-org5f26da5" class="outline-3">
<h3 id="org5f26da5"><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-orgd2ed92b" class="outline-4">
<h4 id="orgd2ed92b"><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-org25629b4" class="outline-4">
<h4 id="org25629b4"><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-org221a287" class="outline-4">
<h4 id="org221a287"><span class="section-number-4">2.2.2</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-orga0220c6" class="outline-4">
<h4 id="orga0220c6"><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-org296c21c" class="outline-4">
<h4 id="org296c21c"><span class="section-number-4">2.2.3</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org4d823b6" class="outline-4">
<h4 id="org4d823b6"><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-orgce97720" class="outline-4">
<h4 id="orgce97720"><span class="section-number-4">2.2.4</span> Read one-electron quantities</h4>
<div id="outline-container-org6d75653" class="outline-4">
<h4 id="org6d75653"><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-org13b8ae6" class="outline-4">
<h4 id="org13b8ae6"><span class="section-number-4">2.2.5</span> Read two-electron quantities</h4>
<div id="outline-container-org79f50e2" class="outline-4">
<h4 id="org79f50e2"><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-org05aa76b" class="outline-5">
<h5 id="org05aa76b"><span class="section-number-5">2.2.5.1</span> Electron repulsion integrals</h5>
<div id="outline-container-orgabfc1a5" class="outline-5">
<h5 id="orgabfc1a5"><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-org7443645" class="outline-5">
<h5 id="org7443645"><span class="section-number-5">2.2.5.2</span> Reduced density matrix</h5>
<div id="outline-container-orgb218809" class="outline-5">
<h5 id="orgb218809"><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-orgdb01e8f" class="outline-4">
<h4 id="orgdb01e8f"><span class="section-number-4">2.2.6</span> Compute the energy</h4>
<div id="outline-container-org4317d8b" class="outline-4">
<h4 id="org4317d8b"><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-org452836b" class="outline-2">
<h2 id="org452836b"><span class="section-number-2">3</span> Reading determinants</h2>
<div id="outline-container-org21b1c8e" class="outline-2">
<h2 id="org21b1c8e"><span class="section-number-2">3</span> Reading determinants</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-orgb4e548b" class="outline-3">
<h3 id="orgb4e548b"><span class="section-number-3">3.1</span> Fortran</h3>
<div id="outline-container-orgc8b0db1" class="outline-3">
<h3 id="orgc8b0db1"><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: 2023-05-22 Mon 10:11</p>
<p class="date">Created: 2023-06-02 Fri 12:01</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>
<!-- 2023-05-22 Mon 10:11 -->
<!-- 2023-06-02 Fri 12:01 -->
<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>
@ -383,7 +383,7 @@ 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: 2023-05-22 Mon 10:11</p>
<p class="date">Created: 2023-06-02 Fri 12:01</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>
<!-- 2023-05-22 Mon 10:11 -->
<!-- 2023-06-02 Fri 12:01 -->
<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: 2023-05-22 Mon 10:11</p>
<p class="date">Created: 2023-06-02 Fri 12:01</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>
<!-- 2023-05-22 Mon 10:11 -->
<!-- 2023-06-02 Fri 12:01 -->
<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="#orge191bc3">1. Format specification</a>
<li><a href="#org9bc4a52">1. Format specification</a>
<ul>
<li><a href="#orgbef2123">1.1. Organization of the data</a></li>
<li><a href="#org90a310f">1.2. Data types</a></li>
<li><a href="#orgf04b1f1">1.1. Organization of the data</a></li>
<li><a href="#org4131aed">1.2. Data types</a></li>
</ul>
</li>
<li><a href="#org6dda4ad">2. The TREXIO library</a>
<li><a href="#orgb2ea255">2. The TREXIO library</a>
<ul>
<li><a href="#org762a802">2.1. The front-end</a></li>
<li><a href="#org64aeb08">2.2. The back-end</a></li>
<li><a href="#org99d975e">2.3. Supported languages</a></li>
<li><a href="#org6b91607">2.4. Source code generation and documentation</a></li>
<li><a href="#orgaf8e742">2.5. Availability</a></li>
<li><a href="#orgb00f349">2.1. The front-end</a></li>
<li><a href="#orgb8eb3a4">2.2. The back-end</a></li>
<li><a href="#org19f3e4c">2.3. Supported languages</a></li>
<li><a href="#org71510dd">2.4. Source code generation and documentation</a></li>
<li><a href="#org79a0751">2.5. Availability</a></li>
</ul>
</li>
</ul>
@ -366,8 +366,8 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-orge191bc3" class="outline-2">
<h2 id="orge191bc3"><span class="section-number-2">1</span> Format specification</h2>
<div id="outline-container-org9bc4a52" class="outline-2">
<h2 id="org9bc4a52"><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-orgbef2123" class="outline-3">
<h3 id="orgbef2123"><span class="section-number-3">1.1</span> Organization of the data</h3>
<div id="outline-container-orgf04b1f1" class="outline-3">
<h3 id="orgf04b1f1"><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-org90a310f" class="outline-3">
<h3 id="org90a310f"><span class="section-number-3">1.2</span> Data types</h3>
<div id="outline-container-org4131aed" class="outline-3">
<h3 id="org4131aed"><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-org6dda4ad" class="outline-2">
<h2 id="org6dda4ad"><span class="section-number-2">2</span> The TREXIO library</h2>
<div id="outline-container-orgb2ea255" class="outline-2">
<h2 id="orgb2ea255"><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-org762a802" class="outline-3">
<h3 id="org762a802"><span class="section-number-3">2.1</span> The front-end</h3>
<div id="outline-container-orgb00f349" class="outline-3">
<h3 id="orgb00f349"><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-org64aeb08" class="outline-3">
<h3 id="org64aeb08"><span class="section-number-3">2.2</span> The back-end</h3>
<div id="outline-container-orgb8eb3a4" class="outline-3">
<h3 id="orgb8eb3a4"><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-org99d975e" class="outline-3">
<h3 id="org99d975e"><span class="section-number-3">2.3</span> Supported languages</h3>
<div id="outline-container-org19f3e4c" class="outline-3">
<h3 id="org19f3e4c"><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-org6b91607" class="outline-3">
<h3 id="org6b91607"><span class="section-number-3">2.4</span> Source code generation and documentation</h3>
<div id="outline-container-org71510dd" class="outline-3">
<h3 id="org71510dd"><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-orgaf8e742" class="outline-3">
<h3 id="orgaf8e742"><span class="section-number-3">2.5</span> Availability</h3>
<div id="outline-container-org79a0751" class="outline-3">
<h3 id="org79a0751"><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: 2023-05-22 Mon 10:11</p>
<p class="date">Created: 2023-06-02 Fri 12:01</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>
<!-- 2023-05-22 Mon 10:11 -->
<!-- 2023-06-02 Fri 12:01 -->
<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="#org207838a">1. Template for HDF5 definitions</a></li>
<li><a href="#org61ceddd">2. Template for HDF5 structures</a></li>
<li><a href="#org6738e80">3. Template for HDF5 init/deinit</a></li>
<li><a href="#orgc836048">4. Template for HDF5 has a group</a></li>
<li><a href="#orgfd7cb8a">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org77ad875">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org83a4556">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#orgbac99a9">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org0b5a6a2">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#orge7276a4">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org4176d38">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#orgb2c09e2">12. Source code for the determinant part</a></li>
<li><a href="#org9d0cc18">13. Helper functions</a></li>
<li><a href="#org240a2c2">1. Template for HDF5 definitions</a></li>
<li><a href="#org04d403c">2. Template for HDF5 structures</a></li>
<li><a href="#orgf9bc3cf">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org7d31f39">4. Template for HDF5 has a group</a></li>
<li><a href="#org2c4e010">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orga1daabf">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org232fd14">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org72650ad">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#orgf52d0e8">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#orgc4b58e4">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org00d1723">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org7904d33">12. Source code for the determinant part</a></li>
<li><a href="#org2a11519">13. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-org207838a" class="outline-2">
<h2 id="org207838a"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-org240a2c2" class="outline-2">
<h2 id="org240a2c2"><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-org61ceddd" class="outline-2">
<h2 id="org61ceddd"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-org04d403c" class="outline-2">
<h2 id="org04d403c"><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-org6738e80" class="outline-2">
<h2 id="org6738e80"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-orgf9bc3cf" class="outline-2">
<h2 id="orgf9bc3cf"><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-orgc836048" class="outline-2">
<h2 id="orgc836048"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-org7d31f39" class="outline-2">
<h2 id="org7d31f39"><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-orgfd7cb8a" class="outline-2">
<h2 id="orgfd7cb8a"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-org2c4e010" class="outline-2">
<h2 id="org2c4e010"><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-org77ad875" class="outline-2">
<h2 id="org77ad875"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-orga1daabf" class="outline-2">
<h2 id="orga1daabf"><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-org83a4556" class="outline-2">
<h2 id="org83a4556"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-org232fd14" class="outline-2">
<h2 id="org232fd14"><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-orgbac99a9" class="outline-2">
<h2 id="orgbac99a9"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div id="outline-container-org72650ad" class="outline-2">
<h2 id="org72650ad"><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-org0b5a6a2" class="outline-2">
<h2 id="org0b5a6a2"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-orgf52d0e8" class="outline-2">
<h2 id="orgf52d0e8"><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-orge7276a4" class="outline-2">
<h2 id="orge7276a4"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-orgc4b58e4" class="outline-2">
<h2 id="orgc4b58e4"><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-org4176d38" class="outline-2">
<h2 id="org4176d38"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-org00d1723" class="outline-2">
<h2 id="org00d1723"><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-orgb2c09e2" class="outline-2">
<h2 id="orgb2c09e2"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div id="outline-container-org7904d33" class="outline-2">
<h2 id="org7904d33"><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-org9d0cc18" class="outline-2">
<h2 id="org9d0cc18"><span class="section-number-2">13</span> Helper functions</h2>
<div id="outline-container-org2a11519" class="outline-2">
<h2 id="org2a11519"><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: 2023-05-22 Mon 10:11</p>
<p class="date">Created: 2023-06-02 Fri 12:01</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="#orgcf5d6d1">1. Template for group-related structures in text back end</a></li>
<li><a href="#orgd324f26">2. Template for general structure in text back end</a></li>
<li><a href="#orgdbf05ad">3. Initialize function (constant part)</a></li>
<li><a href="#org7f37731">4. Deinitialize function (templated part)</a></li>
<li><a href="#orgddc48b0">5. Flush function (templated part)</a></li>
<li><a href="#org9ce3ceb">6. Template for text read a group</a></li>
<li><a href="#org67dffbb">7. Template for text has a group</a></li>
<li><a href="#org3c54689">8. Template for text flush a group</a></li>
<li><a href="#orgee309e8">9. Template for text free memory</a></li>
<li><a href="#orgc14a541">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orgf6564e3">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#org3842cdf">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org2d48931">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org5570ce5">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orgf67d5b8">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#orgca46ab8">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#orgb55e717">17. Source code for the determinant part</a></li>
<li><a href="#org960ac80">1. Template for group-related structures in text back end</a></li>
<li><a href="#org4e8bbd5">2. Template for general structure in text back end</a></li>
<li><a href="#org934a701">3. Initialize function (constant part)</a></li>
<li><a href="#org18a65dc">4. Deinitialize function (templated part)</a></li>
<li><a href="#org459ba20">5. Flush function (templated part)</a></li>
<li><a href="#org5748eed">6. Template for text read a group</a></li>
<li><a href="#org12454f2">7. Template for text has a group</a></li>
<li><a href="#org63bcff0">8. Template for text flush a group</a></li>
<li><a href="#org75a3ce7">9. Template for text free memory</a></li>
<li><a href="#orgcf6f949">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#orgc11570e">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orgfb44446">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org324df1f">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org3301a5d">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#org17c2429">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#orgb7c57fb">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org5230b77">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-orgcf5d6d1" class="outline-2">
<h2 id="orgcf5d6d1"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-org960ac80" class="outline-2">
<h2 id="org960ac80"><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-orgd324f26" class="outline-2">
<h2 id="orgd324f26"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-org4e8bbd5" class="outline-2">
<h2 id="org4e8bbd5"><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-orgdbf05ad" class="outline-2">
<h2 id="orgdbf05ad"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-org934a701" class="outline-2">
<h2 id="org934a701"><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>
@ -597,8 +597,8 @@ In that case, we define an alternate one, which is not as safe as the original o
</div>
</div>
<div id="outline-container-org7f37731" class="outline-2">
<h2 id="org7f37731"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-org18a65dc" class="outline-2">
<h2 id="org18a65dc"><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>
@ -620,8 +620,8 @@ In that case, we define an alternate one, which is not as safe as the original o
</div>
</div>
<div id="outline-container-orgddc48b0" class="outline-2">
<h2 id="orgddc48b0"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div id="outline-container-org459ba20" class="outline-2">
<h2 id="org459ba20"><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>
@ -644,8 +644,8 @@ In that case, we define an alternate one, which is not as safe as the original o
</div>
</div>
<div id="outline-container-org9ce3ceb" class="outline-2">
<h2 id="org9ce3ceb"><span class="section-number-2">6</span> Template for text read a group</h2>
<div id="outline-container-org5748eed" class="outline-2">
<h2 id="org5748eed"><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*
@ -871,8 +871,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
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<h2 id="org67dffbb"><span class="section-number-2">7</span> Template for text has a group</h2>
<div id="outline-container-org12454f2" class="outline-2">
<h2 id="org12454f2"><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>
@ -912,8 +912,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-org3c54689" class="outline-2">
<h2 id="org3c54689"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div id="outline-container-org63bcff0" class="outline-2">
<h2 id="org63bcff0"><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>
@ -977,8 +977,8 @@ trexio_text_read_$group$ (<span style="color: #228b22;">trexio_text_t</span>* <s
</div>
</div>
<div id="outline-container-orgee309e8" class="outline-2">
<h2 id="orgee309e8"><span class="section-number-2">9</span> Template for text free memory</h2>
<div id="outline-container-org75a3ce7" class="outline-2">
<h2 id="org75a3ce7"><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.
@ -1047,8 +1047,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-orgc14a541" class="outline-2">
<h2 id="orgc14a541"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-orgcf6f949" class="outline-2">
<h2 id="orgcf6f949"><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>
@ -1111,8 +1111,8 @@ This function is called upon the non-successful exit from the <code>trexio_text_
</div>
</div>
<div id="outline-container-orgf6564e3" class="outline-2">
<h2 id="orgf6564e3"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-orgc11570e" class="outline-2">
<h2 id="orgc11570e"><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.
@ -1208,8 +1208,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org3842cdf" class="outline-2">
<h2 id="org3842cdf"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-orgfb44446" class="outline-2">
<h2 id="orgfb44446"><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.
@ -1310,8 +1310,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org2d48931" class="outline-2">
<h2 id="org2d48931"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-org324df1f" class="outline-2">
<h2 id="org324df1f"><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>
@ -1385,8 +1385,8 @@ The <code>group_dset</code> array is assumed allocated with the appropriate size
</div>
</div>
</div>
<div id="outline-container-org5570ce5" class="outline-2">
<h2 id="org5570ce5"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-org3301a5d" class="outline-2">
<h2 id="org3301a5d"><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
@ -1676,8 +1676,8 @@ User provides indices and values of the sparse array as two separate variables.
</div>
</div>
<div id="outline-container-orgf67d5b8" class="outline-2">
<h2 id="orgf67d5b8"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div id="outline-container-org17c2429" class="outline-2">
<h2 id="org17c2429"><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
@ -1907,8 +1907,8 @@ Size specifies the number of vector elements to be written.
</div>
</div>
</div>
<div id="outline-container-orgca46ab8" class="outline-2">
<h2 id="orgca46ab8"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-orgb7c57fb" class="outline-2">
<h2 id="orgb7c57fb"><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>
@ -1936,8 +1936,8 @@ Size specifies the number of vector elements to be written.
</div>
</div>
<div id="outline-container-orgb55e717" class="outline-2">
<h2 id="orgb55e717"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div id="outline-container-org5230b77" class="outline-2">
<h2 id="org5230b77"><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
@ -2129,7 +2129,7 @@ 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: 2023-05-22 Mon 10:11</p>
<p class="date">Created: 2023-06-02 Fri 12:01</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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<head>
<!-- 2023-05-22 Mon 10:11 -->
<!-- 2023-06-02 Fri 12:01 -->
<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>
@ -346,70 +346,70 @@ for the JavaScript code in this tag.
<h2>Table of Contents</h2>
<div id="text-table-of-contents">
<ul>
<li><a href="#orgcc4b171">1. Metadata (metadata group)</a></li>
<li><a href="#orgea14af4">2. System</a>
<li><a href="#org9cfa363">1. Metadata (metadata group)</a></li>
<li><a href="#org83a45c6">2. System</a>
<ul>
<li><a href="#orgce3e9a3">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org4b2d478">2.2. Cell (cell group)</a></li>
<li><a href="#org859c35b">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#orgaa749ac">2.4. Electron (electron group)</a></li>
<li><a href="#org1018e1c">2.5. Ground or excited states (state group)</a></li>
<li><a href="#org5eb219e">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#orgda1ae8c">2.2. Cell (cell group)</a></li>
<li><a href="#org48b480c">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#org98668f3">2.4. Electron (electron group)</a></li>
<li><a href="#orga89313d">2.5. Ground or excited states (state group)</a></li>
</ul>
</li>
<li><a href="#org6bb851e">3. Basis functions</a>
<li><a href="#org8c6226a">3. Basis functions</a>
<ul>
<li><a href="#orgbd7427a">3.1. Basis set (basis group)</a>
<li><a href="#orgd6cee43">3.1. Basis set (basis group)</a>
<ul>
<li><a href="#orge8e2855">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#org4f5f173">3.1.2. Plane waves</a></li>
<li><a href="#org3100016">3.1.3. Data definitions</a></li>
<li><a href="#org79a9065">3.1.4. Example</a></li>
<li><a href="#org96bb6be">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#orge25d67e">3.1.2. Plane waves</a></li>
<li><a href="#org2f043c1">3.1.3. Data definitions</a></li>
<li><a href="#org3a25e86">3.1.4. Example</a></li>
</ul>
</li>
<li><a href="#orga4a3e10">3.2. Effective core potentials (ecp group)</a>
<li><a href="#org89ddd44">3.2. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#orgaade331">3.2.1. Example</a></li>
<li><a href="#org053308c">3.2.1. Example</a></li>
</ul>
</li>
<li><a href="#orgc6bff27">3.3. Numerical integration grid (grid group)</a></li>
<li><a href="#org54e4cc2">3.3. Numerical integration grid (grid group)</a></li>
</ul>
</li>
<li><a href="#orgb613b06">4. Orbitals</a>
<li><a href="#org4a32676">4. Orbitals</a>
<ul>
<li><a href="#org822f90a">4.1. Atomic orbitals (ao group)</a>
<li><a href="#org56848ce">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="#org38d002e">4.2. Molecular orbitals (mo group)</a>
<li><a href="#orgae85b3f">4.2. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#orgcf9f871">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org8debca3">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org1b94a0c">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#orgea6b5b7">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org45eab8d">5. Multi-determinant information</a>
<li><a href="#org2b58b7d">5. Multi-determinant information</a>
<ul>
<li><a href="#org42d2faa">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#orgf1c0395">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#org30228f9">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org664970c">5.4. Reduced density matrices (rdm group)</a></li>
<li><a href="#org30c1d28">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org894bca6">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#org2b0e941">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org392be4b">5.4. Reduced density matrices (rdm group)</a></li>
</ul>
</li>
<li><a href="#org52d7528">6. Correlation factors</a>
<li><a href="#org20ef07a">6. Correlation factors</a>
<ul>
<li><a href="#orgf01510f">6.1. Jastrow factor (jastrow group)</a>
<li><a href="#orge62d0f1">6.1. Jastrow factor (jastrow group)</a>
<ul>
<li><a href="#orgff208ef">6.1.1. CHAMP</a></li>
<li><a href="#org31433db">6.1.2. Mu</a></li>
<li><a href="#org6e98f52">6.1.3. Table of values</a></li>
<li><a href="#orgd64809a">6.1.1. CHAMP</a></li>
<li><a href="#orgc212b85">6.1.2. Mu</a></li>
<li><a href="#orgf3d54c3">6.1.3. Table of values</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org5ff2028">7. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#org63ad02e">7. Quantum Monte Carlo data (qmc group)</a></li>
</ul>
</div>
</div>
@ -422,8 +422,8 @@ is reversed in the produced <code>trex.json</code> configuration file as the
library is written in C.
</p>
<div id="outline-container-orgcc4b171" class="outline-2">
<h2 id="orgcc4b171"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-org9cfa363" class="outline-2">
<h2 id="org9cfa363"><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,
@ -433,7 +433,7 @@ have participated to the creation of the file, a list of authors of
the file, and a textual description.
</p>
<table id="org6eb2437" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org7ca9f45" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -516,19 +516,19 @@ value can be manually overwritten (in unsafe mode) from <code>1</code> to <code>
</div>
</div>
<div id="outline-container-orgea14af4" class="outline-2">
<h2 id="orgea14af4"><span class="section-number-2">2</span> System</h2>
<div id="outline-container-org83a45c6" class="outline-2">
<h2 id="org83a45c6"><span class="section-number-2">2</span> System</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-orgce3e9a3" class="outline-3">
<h3 id="orgce3e9a3"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
<div id="outline-container-org5eb219e" class="outline-3">
<h3 id="org5eb219e"><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="orgb590134" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2a10c50" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -595,15 +595,15 @@ given in Cartesian \((x,y,z)\) format.
</div>
</div>
<div id="outline-container-org4b2d478" class="outline-3">
<h3 id="org4b2d478"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
<div id="outline-container-orgda1ae8c" class="outline-3">
<h3 id="orgda1ae8c"><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="org8cbd027" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgace6fea" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -677,15 +677,15 @@ used in periodic calculations.
</div>
</div>
<div id="outline-container-org859c35b" class="outline-3">
<h3 id="org859c35b"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div id="outline-container-org48b480c" class="outline-3">
<h3 id="org48b480c"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div class="outline-text-3" id="text-2-3">
<p>
A single $k$-point per TREXIO file can be stored. The $k$-point is
defined in this group.
</p>
<table id="org707ff16" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org34799fa" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -724,8 +724,8 @@ defined in this group.
</div>
</div>
<div id="outline-container-orgaa749ac" class="outline-3">
<h3 id="orgaa749ac"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
<div id="outline-container-org98668f3" class="outline-3">
<h3 id="org98668f3"><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
@ -744,7 +744,7 @@ the number of &uarr; and &darr; electrons is fixed.
</p>
<table id="org32354cb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5d6afcf" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -790,8 +790,8 @@ the number of &uarr; and &darr; electrons is fixed.
</div>
</div>
<div id="outline-container-org1018e1c" class="outline-3">
<h3 id="org1018e1c"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
<div id="outline-container-orga89313d" class="outline-3">
<h3 id="orga89313d"><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
@ -808,7 +808,7 @@ integrals, etc.
The <code>id</code> and <code>current_label</code> attributes need to be specified for each file.
</p>
<table id="org3f78b36" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2028d58" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -876,16 +876,16 @@ The <code>id</code> and <code>current_label</code> attributes need to be specifi
</div>
</div>
<div id="outline-container-org6bb851e" class="outline-2">
<h2 id="org6bb851e"><span class="section-number-2">3</span> Basis functions</h2>
<div id="outline-container-org8c6226a" class="outline-2">
<h2 id="org8c6226a"><span class="section-number-2">3</span> Basis functions</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-orgbd7427a" class="outline-3">
<h3 id="orgbd7427a"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
<div id="outline-container-orgd6cee43" class="outline-3">
<h3 id="orgd6cee43"><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-orge8e2855" class="outline-4">
<h4 id="orge8e2855"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
<div id="outline-container-org96bb6be" class="outline-4">
<h4 id="org96bb6be"><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
@ -939,8 +939,8 @@ All the basis set parameters are stored in one-dimensional arrays.
</div>
</div>
<div id="outline-container-org4f5f173" class="outline-4">
<h4 id="org4f5f173"><span class="section-number-4">3.1.2</span> Plane waves</h4>
<div id="outline-container-orge25d67e" class="outline-4">
<h4 id="orge25d67e"><span class="section-number-4">3.1.2</span> Plane waves</h4>
<div class="outline-text-4" id="text-3-1-2">
<p>
A plane wave is defined as
@ -961,10 +961,10 @@ plane waves.
</div>
</div>
<div id="outline-container-org3100016" class="outline-4">
<h4 id="org3100016"><span class="section-number-4">3.1.3</span> Data definitions</h4>
<div id="outline-container-org2f043c1" class="outline-4">
<h4 id="org2f043c1"><span class="section-number-4">3.1.3</span> Data definitions</h4>
<div class="outline-text-4" id="text-3-1-3">
<table id="org28e3036" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org83735ab" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1073,8 +1073,8 @@ plane waves.
</div>
</div>
<div id="outline-container-org79a9065" class="outline-4">
<h4 id="org79a9065"><span class="section-number-4">3.1.4</span> Example</h4>
<div id="outline-container-org3a25e86" class="outline-4">
<h4 id="org3a25e86"><span class="section-number-4">3.1.4</span> Example</h4>
<div class="outline-text-4" id="text-3-1-4">
<p>
For example, consider H<sub>2</sub> with the following basis set (in GAMESS
@ -1152,8 +1152,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-orga4a3e10" class="outline-3">
<h3 id="orga4a3e10"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
<div id="outline-container-org89ddd44" class="outline-3">
<h3 id="org89ddd44"><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
@ -1187,7 +1187,7 @@ 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="org2c8ea13" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org2b0e8bd" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1291,8 +1291,8 @@ If you encounter the aforementioned issue, please report it to our
</p>
</div>
<div id="outline-container-orgaade331" class="outline-4">
<h4 id="orgaade331"><span class="section-number-4">3.2.1</span> Example</h4>
<div id="outline-container-org053308c" class="outline-4">
<h4 id="org053308c"><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
@ -1355,8 +1355,8 @@ power = [
</div>
</div>
<div id="outline-container-orgc6bff27" class="outline-3">
<h3 id="orgc6bff27"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
<div id="outline-container-org54e4cc2" class="outline-3">
<h3 id="org54e4cc2"><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
@ -1371,7 +1371,7 @@ 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="org442b360" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd75261d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1488,12 +1488,12 @@ Feel free to submit a PR if you find missing options/functionalities.
</div>
</div>
<div id="outline-container-orgb613b06" class="outline-2">
<h2 id="orgb613b06"><span class="section-number-2">4</span> Orbitals</h2>
<div id="outline-container-org4a32676" class="outline-2">
<h2 id="org4a32676"><span class="section-number-2">4</span> Orbitals</h2>
<div class="outline-text-2" id="text-4">
</div>
<div id="outline-container-org822f90a" class="outline-3">
<h3 id="org822f90a"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
<div id="outline-container-org56848ce" class="outline-3">
<h3 id="org56848ce"><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
@ -1574,7 +1574,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</p>
<table id="orgc0f04af" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc68ca40" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1626,7 +1626,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</table>
</div>
<div id="outline-container-org5e96996" class="outline-4">
<div id="outline-container-org52d25c8" 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">
@ -1644,7 +1644,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="org639fc22" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgc470a22" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1739,7 +1739,7 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-orgf37c08e" class="outline-4">
<div id="outline-container-orgc1c61f3" 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>
@ -1765,7 +1765,7 @@ The Cholesky decomposition of the integrals can also be stored:
\]
</p>
<table id="org62f7f48" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org7b935d2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1833,10 +1833,10 @@ The Cholesky decomposition of the integrals can also be stored:
</div>
</div>
<div id="outline-container-org38d002e" class="outline-3">
<h3 id="org38d002e"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div id="outline-container-orgae85b3f" class="outline-3">
<h3 id="orgae85b3f"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div class="outline-text-3" id="text-4-2">
<table id="org62f199b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgdd82520" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1923,8 +1923,8 @@ The Cholesky decomposition of the integrals can also be stored:
</table>
</div>
<div id="outline-container-orgcf9f871" class="outline-4">
<h4 id="orgcf9f871"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
<div id="outline-container-org1b94a0c" class="outline-4">
<h4 id="org1b94a0c"><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
@ -1932,7 +1932,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="orgd23b370" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd81bc86" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2027,8 +2027,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org8debca3" class="outline-4">
<h4 id="org8debca3"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
<div id="outline-container-orgea6b5b7" class="outline-4">
<h4 id="orgea6b5b7"><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
@ -2036,7 +2036,7 @@ The operators are the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org53580f2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgf4ba5a3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2105,12 +2105,12 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org45eab8d" class="outline-2">
<h2 id="org45eab8d"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div id="outline-container-org2b58b7d" class="outline-2">
<h2 id="org2b58b7d"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div class="outline-text-2" id="text-5">
</div>
<div id="outline-container-org42d2faa" class="outline-3">
<h3 id="org42d2faa"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
<div id="outline-container-org30c1d28" class="outline-3">
<h3 id="org30c1d28"><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 \(\Psi\)
@ -2152,7 +2152,7 @@ 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="org56982f2" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org819b4c8" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2198,8 +2198,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
</div>
</div>
<div id="outline-container-orgf1c0395" class="outline-3">
<h3 id="orgf1c0395"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
<div id="outline-container-org894bca6" class="outline-3">
<h3 id="org894bca6"><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
@ -2221,7 +2221,7 @@ matrix \(\langle D_I | \psi_J \rangle\) needed to project the CSFs in
the basis of Slater determinants.
</p>
<table id="orgacd39a1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge73e8c4" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2267,8 +2267,8 @@ the basis of Slater determinants.
</div>
</div>
<div id="outline-container-org30228f9" class="outline-3">
<h3 id="org30228f9"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
<div id="outline-container-org2b0e941" class="outline-3">
<h3 id="org2b0e941"><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
@ -2339,7 +2339,7 @@ The order of the indices is chosen such that
<li>\(\dots\)</li>
</ul>
<table id="orgd2f8690" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org045f9c3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2420,8 +2420,8 @@ The order of the indices is chosen such that
</div>
</div>
<div id="outline-container-org664970c" class="outline-3">
<h3 id="org664970c"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
<div id="outline-container-org392be4b" class="outline-3">
<h3 id="org392be4b"><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
@ -2493,7 +2493,7 @@ 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="org44d5f4a" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga45559d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2624,12 +2624,12 @@ expressed in a basis of a one-electron function
</div>
</div>
<div id="outline-container-org52d7528" class="outline-2">
<h2 id="org52d7528"><span class="section-number-2">6</span> Correlation factors</h2>
<div id="outline-container-org20ef07a" class="outline-2">
<h2 id="org20ef07a"><span class="section-number-2">6</span> Correlation factors</h2>
<div class="outline-text-2" id="text-6">
</div>
<div id="outline-container-orgf01510f" class="outline-3">
<h3 id="orgf01510f"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
<div id="outline-container-orge62d0f1" class="outline-3">
<h3 id="orge62d0f1"><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
@ -2654,8 +2654,8 @@ following:
</ul>
</div>
<div id="outline-container-orgff208ef" class="outline-4">
<h4 id="orgff208ef"><span class="section-number-4">6.1.1</span> CHAMP</h4>
<div id="outline-container-orgd64809a" class="outline-4">
<h4 id="orgd64809a"><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
@ -2756,8 +2756,8 @@ The terms \(J_{\text{ee},ij}^\infty\) and \(J_{\text{eN}}^\infty\) are shifts to
</div>
<div id="outline-container-org31433db" class="outline-4">
<h4 id="org31433db"><span class="section-number-4">6.1.2</span> Mu</h4>
<div id="outline-container-orgc212b85" class="outline-4">
<h4 id="orgc212b85"><span class="section-number-4">6.1.2</span> Mu</h4>
<div class="outline-text-4" id="text-6-1-2">
<p>
<a href="https://aip.scitation.org/doi/10.1063/5.0044683">Mu-Jastrow</a> is based on a one-parameter correlation factor that has
@ -2854,10 +2854,10 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
</div>
</div>
<div id="outline-container-org6e98f52" class="outline-4">
<h4 id="org6e98f52"><span class="section-number-4">6.1.3</span> Table of values</h4>
<div id="outline-container-orgf3d54c3" class="outline-4">
<h4 id="orgf3d54c3"><span class="section-number-4">6.1.3</span> Table of values</h4>
<div class="outline-text-4" id="text-6-1-3">
<table id="org47fc5e5" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org7bdaa1d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2961,8 +2961,8 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
</div>
</div>
<div id="outline-container-org5ff2028" class="outline-2">
<h2 id="org5ff2028"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
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<h2 id="org63ad02e"><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
@ -2976,7 +2976,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
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@ -3031,7 +3031,7 @@ of $&uarr;$-spin and then all the $&darr;$-spin.
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<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-05-22 Mon 10:11</p>
<p class="date">Created: 2023-06-02 Fri 12:01</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
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