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README.html
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<head>
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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: 2023-05-11 Thu 21:09</p>
<p class="date">Created: 2023-05-11 Thu 21:12</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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<head>
<!-- 2023-05-11 Thu 21:09 -->
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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>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="#orgd483170">1. Writing nuclear coordinates</a>
<li><a href="#orgabecdb0">1. Writing nuclear coordinates</a>
<ul>
<li><a href="#orgd3067b9">1.1. C</a></li>
<li><a href="#orgcadca88">1.2. Python</a></li>
<li><a href="#org7eb2e53">1.3. Fortran</a></li>
<li><a href="#orga0feada">1.1. C</a></li>
<li><a href="#orgb0525dd">1.2. Python</a></li>
<li><a href="#orgb947160">1.3. Fortran</a></li>
</ul>
</li>
<li><a href="#orgf552dbd">2. Accessing sparse quantities (integrals)</a>
<li><a href="#org00880f8">2. Accessing sparse quantities (integrals)</a>
<ul>
<li><a href="#orgd521312">2.1. Fortran</a>
<li><a href="#orgce96664">2.1. Fortran</a>
<ul>
<li><a href="#orgacaf25d">2.1.1. Declare Temporary variables</a></li>
<li><a href="#orge2acdda">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orgb11045d">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org1fa7f25">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#orgf7c5e91">2.1.5. Allocate memory</a></li>
<li><a href="#orge4b883d">2.1.6. Read one-electron quantities</a></li>
<li><a href="#org4ef8a5a">2.1.7. Read two-electron quantities</a>
<li><a href="#orgfb81e77">2.1.1. Declare Temporary variables</a></li>
<li><a href="#orgd74caa7">2.1.2. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org768ca50">2.1.3. Read the nuclear repulsion energy</a></li>
<li><a href="#org6961113">2.1.4. Read the number of molecular orbitals</a></li>
<li><a href="#org5b352e3">2.1.5. Allocate memory</a></li>
<li><a href="#org9472877">2.1.6. Read one-electron quantities</a></li>
<li><a href="#orgc81f28e">2.1.7. Read two-electron quantities</a>
<ul>
<li><a href="#org161bf75">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#orgaceb3d0">2.1.7.2. Reduced density matrix</a></li>
<li><a href="#org6c4424b">2.1.7.1. Electron repulsion integrals</a></li>
<li><a href="#org5d1f8eb">2.1.7.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#orgfb2418d">2.1.8. Compute the energy</a></li>
<li><a href="#org002f16b">2.1.9. Terminate</a></li>
<li><a href="#orgb4958a9">2.1.8. Compute the energy</a></li>
<li><a href="#org910e194">2.1.9. Terminate</a></li>
</ul>
</li>
<li><a href="#org8c572d5">2.2. Python</a>
<li><a href="#org12108a1">2.2. Python</a>
<ul>
<li><a href="#org362db0a">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#orge005dde">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#org9f3edc1">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#orgb5ba7a6">2.2.4. Read one-electron quantities</a></li>
<li><a href="#org244556f">2.2.5. Read two-electron quantities</a>
<li><a href="#org1e60caf">2.2.1. Obtain the name of the TREXIO file from the command line, and open it for reading</a></li>
<li><a href="#org1c7c248">2.2.2. Read the nuclear repulsion energy</a></li>
<li><a href="#orgedeabec">2.2.3. Read the number of molecular orbitals</a></li>
<li><a href="#orgfd9c3b5">2.2.4. Read one-electron quantities</a></li>
<li><a href="#org35dd18e">2.2.5. Read two-electron quantities</a>
<ul>
<li><a href="#orgf07c589">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#org62ca338">2.2.5.2. Reduced density matrix</a></li>
<li><a href="#orgf07700d">2.2.5.1. Electron repulsion integrals</a></li>
<li><a href="#org01647c0">2.2.5.2. Reduced density matrix</a></li>
</ul>
</li>
<li><a href="#org23c6485">2.2.6. Compute the energy</a></li>
<li><a href="#org382e655">2.2.6. Compute the energy</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org0958a70">3. Reading determinants</a>
<li><a href="#org86cac62">3. Reading determinants</a>
<ul>
<li><a href="#org90dbdd6">3.1. Fortran</a></li>
<li><a href="#org66a6dc7">3.1. Fortran</a></li>
</ul>
</li>
</ul>
</div>
</div>
<div id="outline-container-orgd483170" class="outline-2">
<h2 id="orgd483170"><span class="section-number-2">1</span> Writing nuclear coordinates</h2>
<div id="outline-container-orgabecdb0" class="outline-2">
<h2 id="orgabecdb0"><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-orgd3067b9" class="outline-3">
<h3 id="orgd3067b9"><span class="section-number-3">1.1</span> C</h3>
<div id="outline-container-orga0feada" class="outline-3">
<h3 id="orga0feada"><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-orgcadca88" class="outline-3">
<h3 id="orgcadca88"><span class="section-number-3">1.2</span> Python</h3>
<div id="outline-container-orgb0525dd" class="outline-3">
<h3 id="orgb0525dd"><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-org7eb2e53" class="outline-3">
<h3 id="org7eb2e53"><span class="section-number-3">1.3</span> Fortran</h3>
<div id="outline-container-orgb947160" class="outline-3">
<h3 id="orgb947160"><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-orgf552dbd" class="outline-2">
<h2 id="orgf552dbd"><span class="section-number-2">2</span> Accessing sparse quantities (integrals)</h2>
<div id="outline-container-org00880f8" class="outline-2">
<h2 id="org00880f8"><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-orgd521312" class="outline-3">
<h3 id="orgd521312"><span class="section-number-3">2.1</span> Fortran</h3>
<div id="outline-container-orgce96664" class="outline-3">
<h3 id="orgce96664"><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-orgacaf25d" class="outline-4">
<h4 id="orgacaf25d"><span class="section-number-4">2.1.1</span> Declare Temporary variables</h4>
<div id="outline-container-orgfb81e77" class="outline-4">
<h4 id="orgfb81e77"><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-orge2acdda" class="outline-4">
<h4 id="orge2acdda"><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-orgd74caa7" class="outline-4">
<h4 id="orgd74caa7"><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-orgb11045d" class="outline-4">
<h4 id="orgb11045d"><span class="section-number-4">2.1.3</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org768ca50" class="outline-4">
<h4 id="org768ca50"><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-org1fa7f25" class="outline-4">
<h4 id="org1fa7f25"><span class="section-number-4">2.1.4</span> Read the number of molecular orbitals</h4>
<div id="outline-container-org6961113" class="outline-4">
<h4 id="org6961113"><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-orgf7c5e91" class="outline-4">
<h4 id="orgf7c5e91"><span class="section-number-4">2.1.5</span> Allocate memory</h4>
<div id="outline-container-org5b352e3" class="outline-4">
<h4 id="org5b352e3"><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-orge4b883d" class="outline-4">
<h4 id="orge4b883d"><span class="section-number-4">2.1.6</span> Read one-electron quantities</h4>
<div id="outline-container-org9472877" class="outline-4">
<h4 id="org9472877"><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-org4ef8a5a" class="outline-4">
<h4 id="org4ef8a5a"><span class="section-number-4">2.1.7</span> Read two-electron quantities</h4>
<div id="outline-container-orgc81f28e" class="outline-4">
<h4 id="orgc81f28e"><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-org161bf75" class="outline-5">
<h5 id="org161bf75"><span class="section-number-5">2.1.7.1</span> Electron repulsion integrals</h5>
<div id="outline-container-org6c4424b" class="outline-5">
<h5 id="org6c4424b"><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-orgaceb3d0" class="outline-5">
<h5 id="orgaceb3d0"><span class="section-number-5">2.1.7.2</span> Reduced density matrix</h5>
<div id="outline-container-org5d1f8eb" class="outline-5">
<h5 id="org5d1f8eb"><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-orgfb2418d" class="outline-4">
<h4 id="orgfb2418d"><span class="section-number-4">2.1.8</span> Compute the energy</h4>
<div id="outline-container-orgb4958a9" class="outline-4">
<h4 id="orgb4958a9"><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-org002f16b" class="outline-4">
<h4 id="org002f16b"><span class="section-number-4">2.1.9</span> Terminate</h4>
<div id="outline-container-org910e194" class="outline-4">
<h4 id="org910e194"><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-org8c572d5" class="outline-3">
<h3 id="org8c572d5"><span class="section-number-3">2.2</span> Python</h3>
<div id="outline-container-org12108a1" class="outline-3">
<h3 id="org12108a1"><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-org362db0a" class="outline-4">
<h4 id="org362db0a"><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-org1e60caf" class="outline-4">
<h4 id="org1e60caf"><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-orge005dde" class="outline-4">
<h4 id="orge005dde"><span class="section-number-4">2.2.2</span> Read the nuclear repulsion energy</h4>
<div id="outline-container-org1c7c248" class="outline-4">
<h4 id="org1c7c248"><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-org9f3edc1" class="outline-4">
<h4 id="org9f3edc1"><span class="section-number-4">2.2.3</span> Read the number of molecular orbitals</h4>
<div id="outline-container-orgedeabec" class="outline-4">
<h4 id="orgedeabec"><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-orgb5ba7a6" class="outline-4">
<h4 id="orgb5ba7a6"><span class="section-number-4">2.2.4</span> Read one-electron quantities</h4>
<div id="outline-container-orgfd9c3b5" class="outline-4">
<h4 id="orgfd9c3b5"><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-org244556f" class="outline-4">
<h4 id="org244556f"><span class="section-number-4">2.2.5</span> Read two-electron quantities</h4>
<div id="outline-container-org35dd18e" class="outline-4">
<h4 id="org35dd18e"><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-orgf07c589" class="outline-5">
<h5 id="orgf07c589"><span class="section-number-5">2.2.5.1</span> Electron repulsion integrals</h5>
<div id="outline-container-orgf07700d" class="outline-5">
<h5 id="orgf07700d"><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-org62ca338" class="outline-5">
<h5 id="org62ca338"><span class="section-number-5">2.2.5.2</span> Reduced density matrix</h5>
<div id="outline-container-org01647c0" class="outline-5">
<h5 id="org01647c0"><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-org23c6485" class="outline-4">
<h4 id="org23c6485"><span class="section-number-4">2.2.6</span> Compute the energy</h4>
<div id="outline-container-org382e655" class="outline-4">
<h4 id="org382e655"><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-org0958a70" class="outline-2">
<h2 id="org0958a70"><span class="section-number-2">3</span> Reading determinants</h2>
<div id="outline-container-org86cac62" class="outline-2">
<h2 id="org86cac62"><span class="section-number-2">3</span> Reading determinants</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-org90dbdd6" class="outline-3">
<h3 id="org90dbdd6"><span class="section-number-3">3.1</span> Fortran</h3>
<div id="outline-container-org66a6dc7" class="outline-3">
<h3 id="org66a6dc7"><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: 2023-05-11 Thu 21:09</p>
<p class="date">Created: 2023-05-11 Thu 21:12</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>
<!-- 2023-05-11 Thu 21:09 -->
<!-- 2023-05-11 Thu 21:12 -->
<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: 2023-05-11 Thu 21:09</p>
<p class="date">Created: 2023-05-11 Thu 21:12</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>
<!-- 2023-05-11 Thu 21:09 -->
<!-- 2023-05-11 Thu 21:12 -->
<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: 2023-05-11 Thu 21:09</p>
<p class="date">Created: 2023-05-11 Thu 21:12</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
</body>

58
lib.html
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@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en">
<head>
<!-- 2023-05-11 Thu 21:09 -->
<!-- 2023-05-11 Thu 21:12 -->
<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="#org07f0d66">1. Format specification</a>
<li><a href="#org7244862">1. Format specification</a>
<ul>
<li><a href="#orga745592">1.1. Organization of the data</a></li>
<li><a href="#orgc3f6e04">1.2. Data types</a></li>
<li><a href="#orga088805">1.1. Organization of the data</a></li>
<li><a href="#org80c2ccb">1.2. Data types</a></li>
</ul>
</li>
<li><a href="#org1ee1bd5">2. The TREXIO library</a>
<li><a href="#org7263e4d">2. The TREXIO library</a>
<ul>
<li><a href="#org0ce8974">2.1. The front-end</a></li>
<li><a href="#org506e86f">2.2. The back-end</a></li>
<li><a href="#org65baee8">2.3. Supported languages</a></li>
<li><a href="#org350075f">2.4. Source code generation and documentation</a></li>
<li><a href="#org57d7eb6">2.5. Availability</a></li>
<li><a href="#orgb20b53d">2.1. The front-end</a></li>
<li><a href="#org2e5d916">2.2. The back-end</a></li>
<li><a href="#orgd5d49bc">2.3. Supported languages</a></li>
<li><a href="#orgbffecc4">2.4. Source code generation and documentation</a></li>
<li><a href="#org9f4b9bc">2.5. Availability</a></li>
</ul>
</li>
</ul>
@ -366,8 +366,8 @@ for the JavaScript code in this tag.
</div>
<div id="outline-container-org07f0d66" class="outline-2">
<h2 id="org07f0d66"><span class="section-number-2">1</span> Format specification</h2>
<div id="outline-container-org7244862" class="outline-2">
<h2 id="org7244862"><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-orga745592" class="outline-3">
<h3 id="orga745592"><span class="section-number-3">1.1</span> Organization of the data</h3>
<div id="outline-container-orga088805" class="outline-3">
<h3 id="orga088805"><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-orgc3f6e04" class="outline-3">
<h3 id="orgc3f6e04"><span class="section-number-3">1.2</span> Data types</h3>
<div id="outline-container-org80c2ccb" class="outline-3">
<h3 id="org80c2ccb"><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-org1ee1bd5" class="outline-2">
<h2 id="org1ee1bd5"><span class="section-number-2">2</span> The TREXIO library</h2>
<div id="outline-container-org7263e4d" class="outline-2">
<h2 id="org7263e4d"><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-org0ce8974" class="outline-3">
<h3 id="org0ce8974"><span class="section-number-3">2.1</span> The front-end</h3>
<div id="outline-container-orgb20b53d" class="outline-3">
<h3 id="orgb20b53d"><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-org506e86f" class="outline-3">
<h3 id="org506e86f"><span class="section-number-3">2.2</span> The back-end</h3>
<div id="outline-container-org2e5d916" class="outline-3">
<h3 id="org2e5d916"><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-org65baee8" class="outline-3">
<h3 id="org65baee8"><span class="section-number-3">2.3</span> Supported languages</h3>
<div id="outline-container-orgd5d49bc" class="outline-3">
<h3 id="orgd5d49bc"><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-org350075f" class="outline-3">
<h3 id="org350075f"><span class="section-number-3">2.4</span> Source code generation and documentation</h3>
<div id="outline-container-orgbffecc4" class="outline-3">
<h3 id="orgbffecc4"><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-org57d7eb6" class="outline-3">
<h3 id="org57d7eb6"><span class="section-number-3">2.5</span> Availability</h3>
<div id="outline-container-org9f4b9bc" class="outline-3">
<h3 id="org9f4b9bc"><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: 2023-05-11 Thu 21:09</p>
<p class="date">Created: 2023-05-11 Thu 21:12</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>
<!-- 2023-05-11 Thu 21:09 -->
<!-- 2023-05-11 Thu 21:12 -->
<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="#org4a8d822">1. Template for HDF5 definitions</a></li>
<li><a href="#orga8c0143">2. Template for HDF5 structures</a></li>
<li><a href="#orgb364e94">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org4fc4726">4. Template for HDF5 has a group</a></li>
<li><a href="#org169f195">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#org6877ceb">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#orgccdd6e3">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org4c8a231">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#org3576e8b">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org7433fea">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org0faa17e">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org3907e02">12. Source code for the determinant part</a></li>
<li><a href="#org34d0343">13. Helper functions</a></li>
<li><a href="#org757e62d">1. Template for HDF5 definitions</a></li>
<li><a href="#orgdd0440a">2. Template for HDF5 structures</a></li>
<li><a href="#org6d0d0c9">3. Template for HDF5 init/deinit</a></li>
<li><a href="#org391e730">4. Template for HDF5 has a group</a></li>
<li><a href="#org9135634">5. Template for HDF5 has/read/write a numerical attribute</a></li>
<li><a href="#orgc1dc922">6. Template for HDF5 has/read/write a dataset of numerical data</a></li>
<li><a href="#org9e45910">7. Template for HDF5 has/read/write a dataset of sparse data</a></li>
<li><a href="#org215257d">8. Template for HDF5 has/read/write a dataset of buffered vectors</a></li>
<li><a href="#orgd8e1ca7">9. Template for HDF5 has/read/write a dataset of strings</a></li>
<li><a href="#org69c3d7f">10. Template for HDF5 has/read/write a string attribute</a></li>
<li><a href="#org8977ba1">11. Template for HDF5 delete a group (UNSAFE mode)</a></li>
<li><a href="#org8405816">12. Source code for the determinant part</a></li>
<li><a href="#orgf8e2cbd">13. Helper functions</a></li>
</ul>
</div>
</div>
<div id="outline-container-org4a8d822" class="outline-2">
<h2 id="org4a8d822"><span class="section-number-2">1</span> Template for HDF5 definitions</h2>
<div id="outline-container-org757e62d" class="outline-2">
<h2 id="org757e62d"><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-orga8c0143" class="outline-2">
<h2 id="orga8c0143"><span class="section-number-2">2</span> Template for HDF5 structures</h2>
<div id="outline-container-orgdd0440a" class="outline-2">
<h2 id="orgdd0440a"><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-orgb364e94" class="outline-2">
<h2 id="orgb364e94"><span class="section-number-2">3</span> Template for HDF5 init/deinit</h2>
<div id="outline-container-org6d0d0c9" class="outline-2">
<h2 id="org6d0d0c9"><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-org4fc4726" class="outline-2">
<h2 id="org4fc4726"><span class="section-number-2">4</span> Template for HDF5 has a group</h2>
<div id="outline-container-org391e730" class="outline-2">
<h2 id="org391e730"><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-org169f195" class="outline-2">
<h2 id="org169f195"><span class="section-number-2">5</span> Template for HDF5 has/read/write a numerical attribute</h2>
<div id="outline-container-org9135634" class="outline-2">
<h2 id="org9135634"><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-org6877ceb" class="outline-2">
<h2 id="org6877ceb"><span class="section-number-2">6</span> Template for HDF5 has/read/write a dataset of numerical data</h2>
<div id="outline-container-orgc1dc922" class="outline-2">
<h2 id="orgc1dc922"><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-orgccdd6e3" class="outline-2">
<h2 id="orgccdd6e3"><span class="section-number-2">7</span> Template for HDF5 has/read/write a dataset of sparse data</h2>
<div id="outline-container-org9e45910" class="outline-2">
<h2 id="org9e45910"><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
@ -973,8 +973,8 @@ due to the fact that the sparse data will be written in chunks of user-defined s
</div>
</div>
<div id="outline-container-org4c8a231" class="outline-2">
<h2 id="org4c8a231"><span class="section-number-2">8</span> Template for HDF5 has/read/write a dataset of buffered vectors</h2>
<div id="outline-container-org215257d" class="outline-2">
<h2 id="org215257d"><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.
@ -1108,8 +1108,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
<div id="outline-container-org3576e8b" class="outline-2">
<h2 id="org3576e8b"><span class="section-number-2">9</span> Template for HDF5 has/read/write a dataset of strings</h2>
<div id="outline-container-orgd8e1ca7" class="outline-2">
<h2 id="orgd8e1ca7"><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>
@ -1306,8 +1306,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
<div id="outline-container-org7433fea" class="outline-2">
<h2 id="org7433fea"><span class="section-number-2">10</span> Template for HDF5 has/read/write a string attribute</h2>
<div id="outline-container-org69c3d7f" class="outline-2">
<h2 id="org69c3d7f"><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>
@ -1434,8 +1434,8 @@ Chunked I/O in HDF5 for <code>buffered</code> data.
</div>
</div>
</div>
<div id="outline-container-org0faa17e" class="outline-2">
<h2 id="org0faa17e"><span class="section-number-2">11</span> Template for HDF5 delete a group (UNSAFE mode)</h2>
<div id="outline-container-org8977ba1" class="outline-2">
<h2 id="org8977ba1"><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
@ -1475,8 +1475,8 @@ Thus, any corrupted/lost file space will remain in the first file. The use of <c
</div>
</div>
<div id="outline-container-org3907e02" class="outline-2">
<h2 id="org3907e02"><span class="section-number-2">12</span> Source code for the determinant part</h2>
<div id="outline-container-org8405816" class="outline-2">
<h2 id="org8405816"><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.
@ -1578,8 +1578,8 @@ Size specifies the number of data items (e.g. determinants) to process.
</div>
</div>
<div id="outline-container-org34d0343" class="outline-2">
<h2 id="org34d0343"><span class="section-number-2">13</span> Helper functions</h2>
<div id="outline-container-orgf8e2cbd" class="outline-2">
<h2 id="orgf8e2cbd"><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>
@ -1842,7 +1842,7 @@ 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: 2023-05-11 Thu 21:09</p>
<p class="date">Created: 2023-05-11 Thu 21:12</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="#orgdf4c6f0">1. Template for group-related structures in text back end</a></li>
<li><a href="#orgc659ce3">2. Template for general structure in text back end</a></li>
<li><a href="#org1bb8416">3. Initialize function (constant part)</a></li>
<li><a href="#org460582d">4. Deinitialize function (templated part)</a></li>
<li><a href="#orgae15ecb">5. Flush function (templated part)</a></li>
<li><a href="#org1814b77">6. Template for text read a group</a></li>
<li><a href="#org5ab2140">7. Template for text has a group</a></li>
<li><a href="#org563aaa0">8. Template for text flush a group</a></li>
<li><a href="#org7c8b603">9. Template for text free memory</a></li>
<li><a href="#org95be837">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org565da96">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orga8ecbe4">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org519e7da">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org00c414a">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orge868d21">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#org8738c6d">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#orgd504458">17. Source code for the determinant part</a></li>
<li><a href="#orgdf728cb">1. Template for group-related structures in text back end</a></li>
<li><a href="#org7978d09">2. Template for general structure in text back end</a></li>
<li><a href="#org952e5f6">3. Initialize function (constant part)</a></li>
<li><a href="#orgb6d283b">4. Deinitialize function (templated part)</a></li>
<li><a href="#orgae04092">5. Flush function (templated part)</a></li>
<li><a href="#org3915022">6. Template for text read a group</a></li>
<li><a href="#orgd6b2cb9">7. Template for text has a group</a></li>
<li><a href="#orgc316229">8. Template for text flush a group</a></li>
<li><a href="#org36e578e">9. Template for text free memory</a></li>
<li><a href="#org58c7147">10. Template for has/read/write a numerical attribute</a></li>
<li><a href="#org1d3a169">11. Template for has/read/write a dataset of numerical data</a></li>
<li><a href="#orgce4a607">12. Template for has/read/write a dataset of strings</a></li>
<li><a href="#org83915ad">13. Template for has/read/write a string attribute</a></li>
<li><a href="#org74f1884">14. Template for has/read/write the dataset of sparse data</a></li>
<li><a href="#orgdc01240">15. Template for has/read/write a buffered vector</a></li>
<li><a href="#orge963bdf">16. Template for text delete a group (UNSAFE mode)</a></li>
<li><a href="#org8ddb89a">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-orgdf4c6f0" class="outline-2">
<h2 id="orgdf4c6f0"><span class="section-number-2">1</span> Template for group-related structures in text back end</h2>
<div id="outline-container-orgdf728cb" class="outline-2">
<h2 id="orgdf728cb"><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-orgc659ce3" class="outline-2">
<h2 id="orgc659ce3"><span class="section-number-2">2</span> Template for general structure in text back end</h2>
<div id="outline-container-org7978d09" class="outline-2">
<h2 id="org7978d09"><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-org1bb8416" class="outline-2">
<h2 id="org1bb8416"><span class="section-number-2">3</span> Initialize function (constant part)</h2>
<div id="outline-container-org952e5f6" class="outline-2">
<h2 id="org952e5f6"><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-org460582d" class="outline-2">
<h2 id="org460582d"><span class="section-number-2">4</span> Deinitialize function (templated part)</h2>
<div id="outline-container-orgb6d283b" class="outline-2">
<h2 id="orgb6d283b"><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-orgae15ecb" class="outline-2">
<h2 id="orgae15ecb"><span class="section-number-2">5</span> Flush function (templated part)</h2>
<div id="outline-container-orgae04092" class="outline-2">
<h2 id="orgae04092"><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-org1814b77" class="outline-2">
<h2 id="org1814b77"><span class="section-number-2">6</span> Template for text read a group</h2>
<div id="outline-container-org3915022" class="outline-2">
<h2 id="org3915022"><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>
<div id="outline-container-org5ab2140" class="outline-2">
<h2 id="org5ab2140"><span class="section-number-2">7</span> Template for text has a group</h2>
<div id="outline-container-orgd6b2cb9" class="outline-2">
<h2 id="orgd6b2cb9"><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-org563aaa0" class="outline-2">
<h2 id="org563aaa0"><span class="section-number-2">8</span> Template for text flush a group</h2>
<div id="outline-container-orgc316229" class="outline-2">
<h2 id="orgc316229"><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-org7c8b603" class="outline-2">
<h2 id="org7c8b603"><span class="section-number-2">9</span> Template for text free memory</h2>
<div id="outline-container-org36e578e" class="outline-2">
<h2 id="org36e578e"><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-org95be837" class="outline-2">
<h2 id="org95be837"><span class="section-number-2">10</span> Template for has/read/write a numerical attribute</h2>
<div id="outline-container-org58c7147" class="outline-2">
<h2 id="org58c7147"><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-org565da96" class="outline-2">
<h2 id="org565da96"><span class="section-number-2">11</span> Template for has/read/write a dataset of numerical data</h2>
<div id="outline-container-org1d3a169" class="outline-2">
<h2 id="org1d3a169"><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-orga8ecbe4" class="outline-2">
<h2 id="orga8ecbe4"><span class="section-number-2">12</span> Template for has/read/write a dataset of strings</h2>
<div id="outline-container-orgce4a607" class="outline-2">
<h2 id="orgce4a607"><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-org519e7da" class="outline-2">
<h2 id="org519e7da"><span class="section-number-2">13</span> Template for has/read/write a string attribute</h2>
<div id="outline-container-org83915ad" class="outline-2">
<h2 id="org83915ad"><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-org00c414a" class="outline-2">
<h2 id="org00c414a"><span class="section-number-2">14</span> Template for has/read/write the dataset of sparse data</h2>
<div id="outline-container-org74f1884" class="outline-2">
<h2 id="org74f1884"><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-orge868d21" class="outline-2">
<h2 id="orge868d21"><span class="section-number-2">15</span> Template for has/read/write a buffered vector</h2>
<div id="outline-container-orgdc01240" class="outline-2">
<h2 id="orgdc01240"><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-org8738c6d" class="outline-2">
<h2 id="org8738c6d"><span class="section-number-2">16</span> Template for text delete a group (UNSAFE mode)</h2>
<div id="outline-container-orge963bdf" class="outline-2">
<h2 id="orge963bdf"><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-orgd504458" class="outline-2">
<h2 id="orgd504458"><span class="section-number-2">17</span> Source code for the determinant part</h2>
<div id="outline-container-org8ddb89a" class="outline-2">
<h2 id="org8ddb89a"><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: 2023-05-11 Thu 21:09</p>
<p class="date">Created: 2023-05-11 Thu 21:12</p>
<p class="validation"><a href="http://validator.w3.org/check?uri=referer">Validate</a></p>
</div>
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<head>
<!-- 2023-05-11 Thu 21:09 -->
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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>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="#org46fa6da">1. Metadata (metadata group)</a></li>
<li><a href="#org9bba249">2. System</a>
<li><a href="#orgda2288d">1. Metadata (metadata group)</a></li>
<li><a href="#org6c41e63">2. System</a>
<ul>
<li><a href="#orgfbcae59">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org10a399e">2.2. Cell (cell group)</a></li>
<li><a href="#org9fa940d">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#orgf06c669">2.4. Electron (electron group)</a></li>
<li><a href="#org2759d7d">2.5. Ground or excited states (state group)</a></li>
<li><a href="#org0421a2b">2.1. Nucleus (nucleus group)</a></li>
<li><a href="#org29b6ba9">2.2. Cell (cell group)</a></li>
<li><a href="#org2534f89">2.3. Periodic boundary calculations (pbc group)</a></li>
<li><a href="#orgbbf32a9">2.4. Electron (electron group)</a></li>
<li><a href="#org1d0b43f">2.5. Ground or excited states (state group)</a></li>
</ul>
</li>
<li><a href="#org69b2e44">3. Basis functions</a>
<li><a href="#orgcba40b4">3. Basis functions</a>
<ul>
<li><a href="#orgf31b35c">3.1. Basis set (basis group)</a>
<li><a href="#orga101109">3.1. Basis set (basis group)</a>
<ul>
<li><a href="#orgc4cddae">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#org8a079de">3.1.2. Plane waves</a></li>
<li><a href="#org8acd7ae">3.1.3. Data definitions</a></li>
<li><a href="#org77ffcdb">3.1.4. Example</a></li>
<li><a href="#orga17b95d">3.1.1. Gaussian and Slater-type orbitals</a></li>
<li><a href="#orgb5ecd08">3.1.2. Plane waves</a></li>
<li><a href="#org2233d53">3.1.3. Data definitions</a></li>
<li><a href="#org46aa1bd">3.1.4. Example</a></li>
</ul>
</li>
<li><a href="#orgfbe97b4">3.2. Effective core potentials (ecp group)</a>
<li><a href="#org6f82d7f">3.2. Effective core potentials (ecp group)</a>
<ul>
<li><a href="#orge4b31e0">3.2.1. Example</a></li>
<li><a href="#org117cbcd">3.2.1. Example</a></li>
</ul>
</li>
<li><a href="#org8a6d2ab">3.3. Numerical integration grid (grid group)</a></li>
<li><a href="#orgbe9b17a">3.3. Numerical integration grid (grid group)</a></li>
</ul>
</li>
<li><a href="#orge92477e">4. Orbitals</a>
<li><a href="#org3c857aa">4. Orbitals</a>
<ul>
<li><a href="#org0e0214d">4.1. Atomic orbitals (ao group)</a>
<li><a href="#orgf71cd38">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="#org6e93509">4.2. Molecular orbitals (mo group)</a>
<li><a href="#orgd0d1703">4.2. Molecular orbitals (mo group)</a>
<ul>
<li><a href="#org32f50e4">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org62ccd31">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
<li><a href="#org4f438db">4.2.1. One-electron integrals (<code>mo_1e_int</code> group)</a></li>
<li><a href="#org5fd44c2">4.2.2. Two-electron integrals (<code>mo_2e_int</code> group)</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org484dd52">5. Multi-determinant information</a>
<li><a href="#orgcd04623">5. Multi-determinant information</a>
<ul>
<li><a href="#org39461f0">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#org82cd118">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#org2cee9aa">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#orgb09bddc">5.4. Reduced density matrices (rdm group)</a></li>
<li><a href="#org47ba396">5.1. Slater determinants (determinant group)</a></li>
<li><a href="#orgc6f1baf">5.2. Configuration state functions (csf group)</a></li>
<li><a href="#orgdb5deda">5.3. Amplitudes (amplitude group)</a></li>
<li><a href="#org7d22316">5.4. Reduced density matrices (rdm group)</a></li>
</ul>
</li>
<li><a href="#org24a1672">6. Correlation factors</a>
<li><a href="#org80a6885">6. Correlation factors</a>
<ul>
<li><a href="#orgc4059a4">6.1. Jastrow factor (jastrow group)</a>
<li><a href="#org20b99ab">6.1. Jastrow factor (jastrow group)</a>
<ul>
<li><a href="#org281e2d8">6.1.1. CHAMP</a></li>
<li><a href="#orgbfe7e2b">6.1.2. Mu</a></li>
<li><a href="#orgbab30d1">6.1.3. Table of values</a></li>
<li><a href="#orge229364">6.1.1. CHAMP</a></li>
<li><a href="#org71d5586">6.1.2. Mu</a></li>
<li><a href="#org1b5fb91">6.1.3. Table of values</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#org986061a">7. Quantum Monte Carlo data (qmc group)</a></li>
<li><a href="#orgca28771">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-org46fa6da" class="outline-2">
<h2 id="org46fa6da"><span class="section-number-2">1</span> Metadata (metadata group)</h2>
<div id="outline-container-orgda2288d" class="outline-2">
<h2 id="orgda2288d"><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="orgd93442e" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga2f8958" 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-org9bba249" class="outline-2">
<h2 id="org9bba249"><span class="section-number-2">2</span> System</h2>
<div id="outline-container-org6c41e63" class="outline-2">
<h2 id="org6c41e63"><span class="section-number-2">2</span> System</h2>
<div class="outline-text-2" id="text-2">
</div>
<div id="outline-container-orgfbcae59" class="outline-3">
<h3 id="orgfbcae59"><span class="section-number-3">2.1</span> Nucleus (nucleus group)</h3>
<div id="outline-container-org0421a2b" class="outline-3">
<h3 id="org0421a2b"><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="org6cd99ec" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org4c3247f" 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-org10a399e" class="outline-3">
<h3 id="org10a399e"><span class="section-number-3">2.2</span> Cell (cell group)</h3>
<div id="outline-container-org29b6ba9" class="outline-3">
<h3 id="org29b6ba9"><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="org9274c72" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org8dbab8a" 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-org9fa940d" class="outline-3">
<h3 id="org9fa940d"><span class="section-number-3">2.3</span> Periodic boundary calculations (pbc group)</h3>
<div id="outline-container-org2534f89" class="outline-3">
<h3 id="org2534f89"><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="org1300df3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgfc0bb81" 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-orgf06c669" class="outline-3">
<h3 id="orgf06c669"><span class="section-number-3">2.4</span> Electron (electron group)</h3>
<div id="outline-container-orgbbf32a9" class="outline-3">
<h3 id="orgbbf32a9"><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="org921f852" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org921b017" 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-org2759d7d" class="outline-3">
<h3 id="org2759d7d"><span class="section-number-3">2.5</span> Ground or excited states (state group)</h3>
<div id="outline-container-org1d0b43f" class="outline-3">
<h3 id="org1d0b43f"><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="org726cd32" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge53ad77" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -869,16 +869,16 @@ The <code>id</code> and <code>current_label</code> attributes need to be specifi
</div>
</div>
<div id="outline-container-org69b2e44" class="outline-2">
<h2 id="org69b2e44"><span class="section-number-2">3</span> Basis functions</h2>
<div id="outline-container-orgcba40b4" class="outline-2">
<h2 id="orgcba40b4"><span class="section-number-2">3</span> Basis functions</h2>
<div class="outline-text-2" id="text-3">
</div>
<div id="outline-container-orgf31b35c" class="outline-3">
<h3 id="orgf31b35c"><span class="section-number-3">3.1</span> Basis set (basis group)</h3>
<div id="outline-container-orga101109" class="outline-3">
<h3 id="orga101109"><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-orgc4cddae" class="outline-4">
<h4 id="orgc4cddae"><span class="section-number-4">3.1.1</span> Gaussian and Slater-type orbitals</h4>
<div id="outline-container-orga17b95d" class="outline-4">
<h4 id="orga17b95d"><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
@ -932,8 +932,8 @@ All the basis set parameters are stored in one-dimensional arrays.
</div>
</div>
<div id="outline-container-org8a079de" class="outline-4">
<h4 id="org8a079de"><span class="section-number-4">3.1.2</span> Plane waves</h4>
<div id="outline-container-orgb5ecd08" class="outline-4">
<h4 id="orgb5ecd08"><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
@ -954,10 +954,10 @@ plane waves.
</div>
</div>
<div id="outline-container-org8acd7ae" class="outline-4">
<h4 id="org8acd7ae"><span class="section-number-4">3.1.3</span> Data definitions</h4>
<div id="outline-container-org2233d53" class="outline-4">
<h4 id="org2233d53"><span class="section-number-4">3.1.3</span> Data definitions</h4>
<div class="outline-text-4" id="text-3-1-3">
<table id="orgc48c338" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgd238d1c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1066,8 +1066,8 @@ plane waves.
</div>
</div>
<div id="outline-container-org77ffcdb" class="outline-4">
<h4 id="org77ffcdb"><span class="section-number-4">3.1.4</span> Example</h4>
<div id="outline-container-org46aa1bd" class="outline-4">
<h4 id="org46aa1bd"><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
@ -1145,8 +1145,8 @@ prim_factor =
</div>
</div>
<div id="outline-container-orgfbe97b4" class="outline-3">
<h3 id="orgfbe97b4"><span class="section-number-3">3.2</span> Effective core potentials (ecp group)</h3>
<div id="outline-container-org6f82d7f" class="outline-3">
<h3 id="org6f82d7f"><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
@ -1180,7 +1180,7 @@ 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="org06073d3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5a65a25" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1284,8 +1284,8 @@ If you encounter the aforementioned issue, please report it to our
</p>
</div>
<div id="outline-container-orge4b31e0" class="outline-4">
<h4 id="orge4b31e0"><span class="section-number-4">3.2.1</span> Example</h4>
<div id="outline-container-org117cbcd" class="outline-4">
<h4 id="org117cbcd"><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
@ -1348,8 +1348,8 @@ power = [
</div>
</div>
<div id="outline-container-org8a6d2ab" class="outline-3">
<h3 id="org8a6d2ab"><span class="section-number-3">3.3</span> Numerical integration grid (grid group)</h3>
<div id="outline-container-orgbe9b17a" class="outline-3">
<h3 id="orgbe9b17a"><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
@ -1364,7 +1364,7 @@ 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="org49ae3a6" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgb1b85c1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1481,12 +1481,12 @@ Feel free to submit a PR if you find missing options/functionalities.
</div>
</div>
<div id="outline-container-orge92477e" class="outline-2">
<h2 id="orge92477e"><span class="section-number-2">4</span> Orbitals</h2>
<div id="outline-container-org3c857aa" class="outline-2">
<h2 id="org3c857aa"><span class="section-number-2">4</span> Orbitals</h2>
<div class="outline-text-2" id="text-4">
</div>
<div id="outline-container-org0e0214d" class="outline-3">
<h3 id="org0e0214d"><span class="section-number-3">4.1</span> Atomic orbitals (ao group)</h3>
<div id="outline-container-orgf71cd38" class="outline-3">
<h3 id="orgf71cd38"><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
@ -1567,7 +1567,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</p>
<table id="orgffc914b" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org70b9187" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1619,7 +1619,7 @@ AO, so the correction factor \(\mathcal{N}_i'\) for \(d_{xy}\) in the
</table>
</div>
<div id="outline-container-org18fa912" class="outline-4">
<div id="outline-container-org0c1cdf4" 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">
@ -1637,7 +1637,7 @@ The one-electron integrals for a one-electron operator \(\hat{O}\) are
over atomic orbitals.
</p>
<table id="org19691d9" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orga5440fb" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1732,7 +1732,7 @@ over atomic orbitals.
</div>
</div>
<div id="outline-container-org0d97be7" class="outline-4">
<div id="outline-container-orge155873" 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>
@ -1758,7 +1758,7 @@ The Cholesky decomposition of the integrals can also be stored:
\]
</p>
<table id="org4b918ea" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orgfa2feed" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1826,10 +1826,10 @@ The Cholesky decomposition of the integrals can also be stored:
</div>
</div>
<div id="outline-container-org6e93509" class="outline-3">
<h3 id="org6e93509"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div id="outline-container-orgd0d1703" class="outline-3">
<h3 id="orgd0d1703"><span class="section-number-3">4.2</span> Molecular orbitals (mo group)</h3>
<div class="outline-text-3" id="text-4-2">
<table id="org65a9e04" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org3398b96" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -1916,8 +1916,8 @@ The Cholesky decomposition of the integrals can also be stored:
</table>
</div>
<div id="outline-container-org32f50e4" class="outline-4">
<h4 id="org32f50e4"><span class="section-number-4">4.2.1</span> One-electron integrals (<code>mo_1e_int</code> group)</h4>
<div id="outline-container-org4f438db" class="outline-4">
<h4 id="org4f438db"><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
@ -1925,7 +1925,7 @@ The operators as the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="orgb17e57c" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org955cad3" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2020,8 +2020,8 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org62ccd31" class="outline-4">
<h4 id="org62ccd31"><span class="section-number-4">4.2.2</span> Two-electron integrals (<code>mo_2e_int</code> group)</h4>
<div id="outline-container-org5fd44c2" class="outline-4">
<h4 id="org5fd44c2"><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
@ -2029,7 +2029,7 @@ The operators are the same as those defined in the
the basis of molecular orbitals.
</p>
<table id="org650aa8d" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org974d390" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2098,12 +2098,12 @@ the basis of molecular orbitals.
</div>
</div>
<div id="outline-container-org484dd52" class="outline-2">
<h2 id="org484dd52"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div id="outline-container-orgcd04623" class="outline-2">
<h2 id="orgcd04623"><span class="section-number-2">5</span> Multi-determinant information</h2>
<div class="outline-text-2" id="text-5">
</div>
<div id="outline-container-org39461f0" class="outline-3">
<h3 id="org39461f0"><span class="section-number-3">5.1</span> Slater determinants (determinant group)</h3>
<div id="outline-container-org47ba396" class="outline-3">
<h3 id="org47ba396"><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 \(\Psi\)
@ -2145,7 +2145,7 @@ 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="org25041de" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org5b23023" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2191,8 +2191,8 @@ An illustration on how to read determinants is presented in the <a href="./examp
</div>
</div>
<div id="outline-container-org82cd118" class="outline-3">
<h3 id="org82cd118"><span class="section-number-3">5.2</span> Configuration state functions (csf group)</h3>
<div id="outline-container-orgc6f1baf" class="outline-3">
<h3 id="orgc6f1baf"><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
@ -2214,7 +2214,7 @@ matrix \(\langle D_I | \psi_J \rangle\) needed to project the CSFs in
the basis of Slater determinants.
</p>
<table id="org7586896" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge5068a0" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2260,8 +2260,8 @@ the basis of Slater determinants.
</div>
</div>
<div id="outline-container-org2cee9aa" class="outline-3">
<h3 id="org2cee9aa"><span class="section-number-3">5.3</span> Amplitudes (amplitude group)</h3>
<div id="outline-container-orgdb5deda" class="outline-3">
<h3 id="orgdb5deda"><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
@ -2332,7 +2332,7 @@ The order of the indices is chosen such that
<li>\(\dots\)</li>
</ul>
<table id="org968f5da" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org559b3d1" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2413,8 +2413,8 @@ The order of the indices is chosen such that
</div>
</div>
<div id="outline-container-orgb09bddc" class="outline-3">
<h3 id="orgb09bddc"><span class="section-number-3">5.4</span> Reduced density matrices (rdm group)</h3>
<div id="outline-container-org7d22316" class="outline-3">
<h3 id="org7d22316"><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
@ -2486,7 +2486,7 @@ 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="orgf645230" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="orge7d6e45" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2617,12 +2617,12 @@ expressed in a basis of a one-electron function
</div>
</div>
<div id="outline-container-org24a1672" class="outline-2">
<h2 id="org24a1672"><span class="section-number-2">6</span> Correlation factors</h2>
<div id="outline-container-org80a6885" class="outline-2">
<h2 id="org80a6885"><span class="section-number-2">6</span> Correlation factors</h2>
<div class="outline-text-2" id="text-6">
</div>
<div id="outline-container-orgc4059a4" class="outline-3">
<h3 id="orgc4059a4"><span class="section-number-3">6.1</span> Jastrow factor (jastrow group)</h3>
<div id="outline-container-org20b99ab" class="outline-3">
<h3 id="org20b99ab"><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
@ -2647,8 +2647,8 @@ following:
</ul>
</div>
<div id="outline-container-org281e2d8" class="outline-4">
<h4 id="org281e2d8"><span class="section-number-4">6.1.1</span> CHAMP</h4>
<div id="outline-container-orge229364" class="outline-4">
<h4 id="orge229364"><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
@ -2749,8 +2749,8 @@ The terms \(J_{\text{ee},ij}^\infty\) and \(J_{\text{eN}}^\infty\) are shifts to
</div>
<div id="outline-container-orgbfe7e2b" class="outline-4">
<h4 id="orgbfe7e2b"><span class="section-number-4">6.1.2</span> Mu</h4>
<div id="outline-container-org71d5586" class="outline-4">
<h4 id="org71d5586"><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
@ -2847,10 +2847,10 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
</div>
</div>
<div id="outline-container-orgbab30d1" class="outline-4">
<h4 id="orgbab30d1"><span class="section-number-4">6.1.3</span> Table of values</h4>
<div id="outline-container-org1b5fb91" class="outline-4">
<h4 id="org1b5fb91"><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="org0da0045" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<table id="org7b94cdf" border="2" cellspacing="0" cellpadding="6" rules="groups" frame="hsides">
<colgroup>
@ -2954,8 +2954,8 @@ The parameter \(\mu\) is stored in the <code>ee</code> array, the parameters
</div>
</div>
<div id="outline-container-org986061a" class="outline-2">
<h2 id="org986061a"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
<div id="outline-container-orgca28771" class="outline-2">
<h2 id="orgca28771"><span class="section-number-2">7</span> Quantum Monte Carlo data (qmc group)</h2>
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In quantum Monte Carlo calculations, the wave function is evaluated
@ -2969,7 +2969,7 @@ By convention, the electron coordinates contain first all the electrons
of $&uarr;$-spin and then all the $&darr;$-spin.
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@ -3024,7 +3024,7 @@ of $&uarr;$-spin and then all the $&darr;$-spin.
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<p class="author">Author: TREX-CoE</p>
<p class="date">Created: 2023-05-11 Thu 21:09</p>
<p class="date">Created: 2023-05-11 Thu 21:12</p>
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